Essential Cell Biology

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ESSENTIAL CELL BIOLOGY
S • BRAY
ESSENTIAL
CELL BIOLOGY
GARLAND SCIENCE
ESSENTIAL
CELL BIOLOGY
•
ROB
FOURTH
EDITION
FOUrTh EDiTiON
FOURTH EDITION
•
HO
IN
JO
RA
FF
PK
ALBERTS • BRAY • HOPKIN • JOHNSON
LEWIS • RAFF • ROBERTS • WALTER
•
HN
SON
•
I
W
E
L
S
•
ISBN 978-0-8153-4455-1
9 780815 344551
ecb4_cover_soft.indd 1
ECB4 interactive DVD-ROM inside
11/09/2013 13:25
FOURTH EDITION
ESSENTIAL
CELL BIOLOGY
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FOURTH EDITION
ESSENTIAL
CELL BIOLOGY
ALBERTS • BRAY • HOPKIN • JOHNSON • LEWIS • RAFF • ROBERTS • WALTER
Garland Science
Vice President: Denise Schanck
Senior Editor: Michael Morales
Production Editor and Layout: Emma Jeffcock of EJ Publishing
Services
Illustrator: Nigel Orme
Developmental Editor: Monica Toledo
Editorial Assistants: Lamia Harik and Alina Yurova
Copy Editor: Jo Clayton
Book Design: Matthew McClements, Blink Studio, Ltd.
Cover Illustration: Jose Ortega
Authors Album Cover: Photography, Christophe Carlinet;
Design, Nigel Orme
Indexer: Bill Johncocks
© 2014 by Bruce Alberts, Dennis Bray, Karen Hopkin,
Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
and Peter Walter
© 2010 by Bruce Alberts, Dennis Bray, Karen Hopkin,
Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
and Peter Walter
© 2004 by Bruce Alberts, Dennis Bray, Karen Hopkin,
Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
and Peter Walter
© 1998 by Bruce Alberts, Dennis Bray, Alexander Johnson,
Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter
This book contains information obtained from authentic and
highly regarded sources. Every effort has been made to trace
copyright holders and to obtain their permission for the use of
copyright material. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are
listed. Reasonable efforts have been made to publish reliable
data and information, but the author and the publisher cannot
assume responsibility for the validity of all materials or for the
consequences of their use.
Essential Cell Biology Website
Artistic and Scientific Direction: Peter Walter
Narrated by: Julie Theriot
Producer: Michael Morales
About the Authors
Bruce Alberts received his PhD from Harvard University
and is the Chancellor’s Leadership Chair in Biochemistry
and Biophysics for Science and Education, University of
California, San Francisco. He was the editor-in-chief of
Science magazine from 2008–2013, and for twelve years
he served as President of the U.S. National Academy of
Sciences (1993–2005).
Dennis Bray received his PhD from Massachusetts Institute
of Technology and is currently an active emeritus professor
at the University of Cambridge.
Karen Hopkin received her PhD in biochemistry from
the Albert Einstein College of Medicine and is a science
writer in Somerville, Massachusetts. She is a contributor to
Scientific American’s daily podcast, 60-Second Science, and to
E. O. Wilson’s digital biology textbook, Life on Earth.
Alexander Johnson received his PhD from Harvard
University and is Professor of Microbiology and Immunology
at the University of California, San Francisco.
Julian Lewis received his DPhil from the University of
Oxford and is an Emeritus Scientist at the London Research
Institute of Cancer Research UK.
Martin Raff received his MD from McGill University and is
at the Medical Research Council Laboratory for Molecular
Cell Biology and Cell Biology Unit at University College
London.
Keith Roberts received his PhD from the University of
Cambridge and was Deputy Director of the John Innes
Centre, Norwich. He is currently Emeritus Professor at the
University of East Anglia.
Peter Walter received his PhD from The Rockefeller
University in New York and is Professor of the Department
of Biochemistry and Biophysics at the University of
California, San Francisco, and an Investigator of the Howard
Hughes Medical Institute.
All rights reserved. No part of this book covered by the copyright hereon may be reproduced or used in any format in any
form or by any means—graphic, electronic, or mechanical, including photocopying, recording, taping, or information storage
and retrieval systems—without permission of the publisher.
ISBNs: 978-0-8153-4454-4 (hardcover); 978-0-8153-4455-1
(softcover).
Published by Garland Science, Taylor & Francis Group, LLC,
an informa business, 711 Third Avenue, New York, NY 10017,
USA, and 3 Park Square, Milton Park, Abingdon, OX14 4RN, UK.
Printed in the United States of America
15 14 13 12 11 10 9 8 7 6 5 4 3 2 1
Visit our website at http://www.garlandscience.com
Library of Congress Cataloging-in-Publication Data
Alberts, Bruce.
Essential cell biology / Bruce Alberts [and seven others].
-- Fourth edition.
pages cm.
ISBN 978-0-8153-4454-4 (hardback)
1. Cytology. 2. Molecular biology. 3. Biochemistry. I. Title.
QH581.2.E78 2013
571.6--dc23
2013025976
v
Preface
In our world there is no form of matter more astonishing than the living cell: tiny, fragile, marvelously intricate, continually made afresh, yet
preserving in its DNA a record of information dating back more than
three billion years, to a time when our planet had barely cooled from
the hot materials of the nascent solar system. Ceaselessly re-engineered
and diversified by evolution, extraordinarily versatile and adaptable, the
cell retains a complex core of self-replicating chemical machinery that is
shared and endlessly repeated by every living organism on the face of the
Earth—in every animal, every leaf, every bacterium in a piece of cheese,
every yeast in a vat of wine.
Curiosity, if nothing else, should drive us to study cell biology; we need to
understand cell biology to understand ourselves. But there are practical
reasons, too, why cell biology should be a part of everyone’s education.
We are made of cells, we feed on cells, and our world is made habitable by cells. The challenge for scientists is to deepen our knowledge of
cells and find new ways to apply it. All of us, as citizens, need to know
something of the subject to grapple with the modern world, from our
own health affairs to the great public issues of environmental change,
biomedical technologies, agriculture, and epidemic disease.
Cell biology is a big subject, and it has links with almost every other branch
of science. The study of cell biology therefore provides a great scientific
education. However, as the science advances, it becomes increasingly
easy to become lost in detail, distracted by an overload of information
and technical terminology. In this book we therefore focus on providing
a digestible, straightforward, and engaging account of only the essential
principles. We seek to explain, in a way that can be understood even by
a reader approaching biology for the first time, how the living cell works:
to show how the molecules of the cell—especially the protein, DNA, and
RNA molecules—cooperate to create this remarkable system that feeds,
responds to stimuli, moves, grows, divides, and duplicates itself.
The need for a clear account of the essentials of cell biology became
apparent to us while we were writing Molecular Biology of the Cell (MBoC),
now in its fifth edition. MBoC is a large book aimed at advanced undergraduates and graduate students specializing in the life sciences or
medicine. Many students and educated lay people who require an introductory account of cell biology would find MBoC too detailed for their
needs. Essential Cell Biology (ECB), in contrast, is designed to provide the
fundamentals of cell biology that are required by anyone to understand
both the biomedical and the broader biological issues that affect our lives.
This fourth edition has been extensively revised. We have brought every
part of the book up to date, with new material on regulatory RNAs,
induced pluripotent stem cells, cell suicide and reprogramming, the
human genome, and even Neanderthal DNA. In response to student
feedback, we have improved our discussions of photosynthesis and DNA
vi
Preface
repair. We have added many new figures and have updated our coverage of many exciting new experimental techniques—including RNAi,
optogenetics, the applications of new DNA sequencing technologies, and
the use of mutant organisms to probe the defects underlying human disease. At the same time, our “How We Know” sections continue to present
experimental data and design, illustrating with specific examples how
biologists tackle important questions and how their experimental results
shape future ideas.
As before, the diagrams in ECB emphasize central concepts and are
stripped of unnecessary details. The key terms introduced in each chapter
are highlighted when they first appear and are collected together at the
end of the book in a large, illustrated glossary.
A central feature of the book is the many questions that are presented in
the text margins and at the end of each chapter. These are designed to
provoke students to think carefully about what they have read, encouraging them to pause and test their understanding. Many questions challenge
the student to place the newly acquired information in a broader biological context, and some have more than one valid answer. Others invite
speculation. Answers to all the questions are given at the end of the book;
in many cases these provide a commentary or an alternative perspective
on material presented in the main text.
For those who want to develop their active grasp of cell biology further,
we recommend Molecular Biology of the Cell, Fifth Edition: A Problems
Approach, by John Wilson and Tim Hunt. Though written as a companion to MBoC, this book contains questions at all levels of difficulty and
contains a goldmine of thought-provoking problems for teachers and
students. We have drawn upon it for some of the questions in ECB, and
we are very grateful to its authors.
The explosion of new imaging and computer technologies continues
to provide fresh and spectacular views of the inner workings of living
cells. We have captured some of this excitement in the new Essential Cell
Biology website, located at www.garlandscience.com/ECB4-students. This
site, which is freely available to anyone in the world with an interest in
cell biology, contains over 150 video clips, animations, molecular structures, and high-resolution micrographs—all designed to complement the
material in individual book chapters. One cannot watch cells crawling,
dividing, segregating their chromosomes, or rearranging their surface
without a sense of wonder at the molecular mechanisms that underlie
these processes. For a vivid sense of the marvel that science reveals, it
is hard to match the narrated movie of DNA replication. These resources
have been carefully designed to make the learning of cell biology both
easier and more rewarding.
Those who seek references for further reading will find them on the ECB
student and instructor websites. But for the very latest reviews in the current literature, we suggest the use of web-based search engines, such as
PubMed (www.ncbi.nlm.nih.gov) or Google Scholar (scholar.google.com).
As with MBoC, each chapter of ECB is the product of a communal
effort, with individual drafts circulating from one author to another. In
addition, many people have helped us, and these are credited in the
Acknowledgments that follow. Despite our best efforts, it is inevitable
that there will be errors in the book. We encourage readers who find them
to let us know at [email protected], so that we can correct these
errors in the next printing.
vii
Acknowledgments
The authors acknowledge the many contributions of
professors and students from around the world in the
creation of this fourth edition. In particular, we are grateful to the students who participated in our focus groups;
they provided invaluable feedback about their experiences using the book and our multimedia, and many of
their suggestions were implemented in this edition.
We would also like to thank the professors who helped
organize the student focus groups at their schools:
Nancy W. Kleckner at Bates College, Kate Wright and
Dina Newman at Rochester Institute of Technology,
David L. Gard at University of Utah, and Chris Brandl
and Derek McLachlin at University of Western Ontario.
We greatly appreciate their hospitality and the opportunity to learn from their students.
We also received detailed reviews from many instructors who used the third edition, and we would like to
thank them for their contributions: Devavani Chatterjea,
Macalester College; Frank Hauser, University of
Copenhagen; Alan Jones, University of North Carolina at
Chapel Hill; Eugene Mesco, Savannah State University;
M. Scott Shell, University of California Santa Barbara;
Grith Lykke Sørensen, University of Southern Denmark;
Marta Bechtel, James Madison University; David
Bourgaize, Whittier College; John Stephen Horton,
Union College; Sieirn Lim, Nanyang Technological
University; Satoru Kenneth Nishimoto, University of
Tennessee Health Science Center; Maureen Peters,
Oberlin College; Johanna Rees, University of Cambridge;
Gregg Whitworth, Grinnell College; Karl Fath, Queens
College, City University of New York; Barbara Frank,
Idaho State University; Sarah Lundin-Schiller, Austin
Peay State University; Marianna Patrauchan, Oklahoma
State University; Ellen Rosenberg, University of British
Columbia; Leslie Kate Wright, Rochester Institute of
Technology; Steven H. Denison, Eckerd College; David
Featherstone, University of Illinois at Chicago; Andor
Kiss, Miami University; Julie Lively, Sewanee, The
University of the South; Matthew Rainbow, Antelope
Valley College; Juliet Spencer, University of San Francisco;
Christoph Winkler, National University of Singapore;
Richard Bird, Auburn University; David Burgess, Boston
College; Elisabeth Cox, State University of New York,
College at Geneseo; David L. Gard, University of Utah;
Beatrice Holton, University of Wisconsin Oshkosh; Glenn
H. Kageyama, California State Polytechnic University,
Pomona; Jane R. Dunlevy, University of North Dakota;
Matthias Falk, Lehigh University. We also want to thank
James Hadfield of Cancer Research UK Cambridge
Institute for his review of the methods chapter.
Special thanks go to David Morgan, a coauthor of MBoC,
for his help on the signaling and cell division chapters.
We are very grateful, too, to the readers who alerted us
to errors they had found in the previous edition.
Many staff at Garland Science contributed to the creation of this book and made our work on it a pleasure.
First of all, we owe a special debt to Michael Morales,
our editor, who coordinated the whole enterprise. He
organized the initial reviewing and the focus groups,
worked closely with the authors on their chapters,
urged us on when we fell behind, and played a major
part in the design, assembly, and production of Essential
Cell Biology student website. Monica Toledo managed
the flow of chapters through the book development
and production process, and oversaw the writing of
the accompanying question bank. Lamia Harik gave
editorial assistance. Nigel Orme took original drawings created by author Keith Roberts and redrew them
on a computer, or occasionally by hand, with great
skill and flair. To Matt McClements goes the credit for
the graphic design of the book and the creation of the
chapter-opener sculptures. As in previous editions,
Emma Jeffcock did a brilliant job in laying out the whole
book and meticulously incorporating our endless corrections. Adam Sendroff and Lucy Brodie gathered user
feedback and launched the book into the wide world.
Denise Schanck, the Vice President of Garland Science,
attended all of our writing retreats and orchestrated
everything with great taste and diplomacy. We give our
thanks to everyone in this long list.
Last but not least, we are grateful, yet again, to our colleagues and our families for their unflagging tolerance
and support.
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ix
Resources for Instructors and Students
The teaching and learning resources for instructors and
students are available online. The instructor’s resources
are password protected and available only to qualified instructors. The student resources are available to
everyone. We hope these resources will enhance student
learning, and make it easier for instructors to prepare
dynamic lectures and activities for the classroom.
Instructor Resources
Instructor Resources are available on the Garland
Science Instructor’s Resource Site, located at www.
garlandscience.com/instructors. The website provides
access not only to the teaching resources for this book
but also to all other Garland Science textbooks. Qualified
instructors can obtain access to the site from their sales
representative or by emailing [email protected]
Question Bank
Written by Linda Huang, University of Massachusetts,
Boston, and Cheryl D. Vaughan, Harvard University
Division of Continuing Education, the revised and
expanded question bank includes a variety of question
formats: multiple choice, fill-in-the-blank, true-false,
matching, essay, and challenging “thought” questions.
There are approximately 60–70 questions per chapter,
and a large number of the multiple-choice questions
will be suitable for use with personal response systems
(that is, clickers). The Question Bank was created with
the philosophy that a good exam should do much more
than simply test students’ ability to memorize information; it should require them to reflect upon and integrate
information as a part of a sound understanding. It provides a comprehensive sampling of questions that can
be used either directly or as inspiration for instructors to
write their own test questions.
Art of Essential Cell Biology, Fourth Edition
References
The images from the book are available in two convenient formats: PowerPoint® and JPEG. They have been
optimized for display on a computer. Figures are searchable by figure number, figure name, or by keywords used
in the figure legend from the book.
Adapted from the detailed references of Molecular
Biology of the Cell, and organized by the table of contents for Essential Cell Biology, the “References” provide
a rich compendium of journal and review articles for reference and reading assignments. The “References” PDF
document is available on both the instructor and student
websites.
Figure-Integrated Lecture Outlines
The section headings, concept headings, and figures
from the text have been integrated into PowerPoint
presentations. These will be useful for instructors who
would like a head start creating lectures for their course.
Like all of our PowerPoint presentations, the lecture
outlines can be customized. For example, the content
of these presentations can be combined with videos and
questions from the book or “Question Bank,” in order to
create unique lectures that facilitate interactive learning.
Animations and Videos
The 130+ animations and videos that are available to
students are also available on the Instructor’s Resource
site in two formats. The WMV-formatted movies are
created for instructors who wish to use the movies in
PowerPoint presentations on Windows® computers; the
QuickTime-formatted movies are for use in PowerPoint
for Apple computers or Keynote® presentations. The
movies can easily be downloaded to your computer
using the “download” button on the movie preview page.
Medical Topics Guide
This document highlights medically relevant topics covered throughout the book, and will be particularly useful
for instructors with a large number of premedical, health
science, or nursing students.
Media Guide
This document overviews the multimedia available for
students and instructors and contains the text of the
voice-over narration for all of the movies.
Blackboard® and LMS Integration
The movies, book images, and student assessments that
accompany the book can be integrated into Blackboard
or other learning management systems. These resources
are bundled into a “Common Cartridge” that facilitates
bulk uploading of textbook resources into Blackboard and
other learning management systems. The LMS Common
Cartridge can be obtained on a DVD from your sales representative or by emailing [email protected]
x
Resources for Instructors and Students
Student Resources
The resources for students are available on the Essential
Cell Biology Student Website, located at www.garland
science.com/ECB4-students.
Animations and Videos
There are over 130 movies, covering a wide range of cell
biology topics, which review key concepts in the book
and illuminate the cellular microcosm.
Student Self-Assessments
The website contains a variety of self-assessment tools
to help students.
•
Each chapter has a multiple-choice quiz to test
basic reading comprehension.
•
There are also a number of media assessments that
require students to respond to specific questions
about movies on the website or figures in the book.
•
Additional concept questions complement the
questions available in the book.
•
“Challenge” questions are included that provide a
more experimental perspective or require a greater
depth of conceptual understanding.
Cell Explorer
This application teaches cell morphology through interactive micrographs that highlight important cellular
structures.
Flashcards
Each chapter contains a set of flashcards, built into the
website, that allow students to review key terms from
the text.
Glossary
The complete glossary from the book is available on the
website and can be searched or browsed.
References
A set of references is available for each chapter for further reading and exploration.
xi
Contents and Special Features
Chapter 1 Cells: The Fundamental Units of Life
Panel 1–1 Microscopy
Panel 1–2 Cell Architecture
How We Know: Life’s Common Mechanisms
Chapter 2 Chemical Components of Cells
How We Know: What Are Macromolecules?
Panel 2–1 Chemical Bonds and Groups
Panel 2–2 The Chemical Properties of Water
Panel 2–3 An Outline of Some of the Types of Sugars
Panel 2–4 Fatty Acids and Other Lipids
Panel 2–5 The 20 Amino Acids Found in Proteins
Panel 2–6 A Survey of the Nucleotides
Panel 2–7 The Principal Types of Weak Noncovalent Bonds
Chapter 3 Energy, Catalysis, and Biosynthesis
Panel 3–1 Free Energy and Biological Reactions
How We Know: Measuring Enzyme Performance
Chapter 4 Protein Structure and Function
Panel 4–1 A Few Examples of Some General Protein Functions
Panel 4–2 Making and Using Antibodies
How We Know: Probing Protein Structure
Panel 4–3 Cell Breakage and Initial Fractionation of Cell Extracts
Panel 4–4 Protein Separation by Chromatography
Panel 4–5 Protein Separation by Electrophoresis
Chapter 5 DNA and Chromosomes
How We Know: Genes Are Made of DNA
Chapter 6 DNA Replication, Repair, and Recombination
How We Know: The Nature of Replication
Chapter 7 From DNA to Protein: How Cells Read the Genome
1
10–11
25
30–31
39
60–61
66–67
68–69
70–71
72–73
74–75
76–77
78–79
83
96–97
104–106
121
122
146–147
162–163
164–165
166
167
171
174–176
197
200–202
223
How We Know: Cracking the Genetic Code
240–241
Chapter 8 Control of Gene Expression
261
How We Know: Gene Regulation—the Story of Eve
Chapter 9 How Genes and Genomes Evolve
How We Know: Counting Genes
274–275
289
316–317
xii
Contents and Special Features
Chapter 10 Modern Recombinant DNA Technology
How We Know: Sequencing The Human Genome
Chapter 11 Membrane Structure
How We Know: Measuring Membrane Flow
Chapter 12 Transport Across Cell Membranes
How We Know: Squid Reveal Secrets of Membrane Excitability
Chapter 13 How Cells Obtain Energy From Food
Panel 13–1 Details of the 10 Steps of Glycolysis
Panel 13–2 The Complete Citric Acid Cycle
How We Know: Unraveling the Citric Acid Cycle
Chapter 14 Energy Generation in Mitochondria and Chloroplasts
How We Know: How Chemiosmotic Coupling Drives ATP Synthesis
Panel 14–1 Redox Potentials
Chapter 15 Intracellular Compartments and Protein Transport
How We Know: Tracking Protein and Vesicle Transport
Chapter 16 Cell Signaling
How We Know: Untangling Cell Signaling Pathways
Chapter 17 Cytoskeleton
How We Know: Pursuing Microtubule-Associated Motor Proteins
Chapter 18 The Cell-Division Cycle
How We Know: Discovery of Cyclins and Cdks
Panel 18–1 The Principal Stages of M Phase in an Animal Cell
Chapter 19 Sexual Reproduction and the Power of Genetics
Panel 19–1 Some Essentials of Classical Genetics
How We Know: Using SNPs To Get a Handle on Human Disease
Chapter 20 Cell Communities: Tissues, Stem Cells, and Cancer
How We Know: Making Sense of the Genes That Are Critical for Cancer
325
344–345
359
378–379
383
406–407
419
428–429
434–435
436–437
447
462–463
466
487
512–513
525
556–557
565
580–581
603
609–610
622–623
645
669
676–677
683
722–723
xiii
Detailed Contents
Chapter 1
Cells: The Fundamental Units of Life
1
Unity and Diversity of Cells
Cells Vary Enormously in Appearance and Function
Living Cells All Have a Similar Basic Chemistry
All Present-Day Cells Have Apparently Evolved
from the Same Ancestral Cell
Genes Provide the Instructions for Cell Form,
Function, and Complex Behavior
2
2
3
Cells Under the Microscope
The Invention of the Light Microscope Led to the
Discovery of Cells
Light Microscopes Allow Examination of Cells
and Some of Their Components
The Fine Structure of a Cell Is Revealed by
Electron Microscopy
5
4
5
6
7
8
The Prokaryotic Cell
12
Prokaryotes Are the Most Diverse and Numerous
Cells on Earth
13
The World of Prokaryotes Is Divided into Two
Domains: Bacteria and Archaea
15
The Eukaryotic Cell
The Nucleus Is the Information Store of the Cell
Mitochondria Generate Usable Energy from
Food to Power the Cell
Chloroplasts Capture Energy from Sunlight
Internal Membranes Create Intracellular
Compartments with Different Functions
The Cytosol Is a Concentrated Aqueous Gel
of Large and Small Molecules
The Cytoskeleton Is Responsible for Directed
Cell Movements
The Cytoplasm Is Far from Static
Eukaryotic Cells May Have Originated as
Predators
15
15
Model Organisms
Molecular Biologists Have Focused on E. coli
Brewer’s Yeast Is a Simple Eukaryotic Cell
Arabidopsis Has Been Chosen as a Model Plant
Model Animals Include Flies, Fish, Worms,
and Mice
Biologists Also Directly Study Human Beings
and Their Cells
26
27
27
28
16
18
19
21
21
22
23
28
32
Comparing Genome Sequences Reveals Life’s
Common Heritage
Genomes Contain More Than Just Genes
33
35
Essential Concepts
35
Questions
37
Chapter 2
Chemical Components of Cells
39
Chemical Bonds
Cells Are Made of Relatively Few Types of Atoms
The Outermost Electrons Determine How Atoms
Interact
Covalent Bonds Form by the Sharing of Electrons
There Are Different Types of Covalent Bonds
Covalent Bonds Vary in Strength
Ionic Bonds Form by the Gain and Loss of
Electrons
Noncovalent Bonds Help Bring Molecules
Together in Cells
Hydrogen Bonds Are Important Noncovalent
Bonds For Many Biological Molecules
Some Polar Molecules Form Acids and Bases
in Water
40
40
SMALL Molecules in Cells
A Cell Is Formed from Carbon Compounds
Cells Contain Four Major Families of Small
Organic Molecules
Sugars Are Both Energy Sources and Subunits
of Polysaccharides
Fatty Acid Chains Are Components of Cell
Membranes
Amino Acids Are the Subunits of Proteins
Nucleotides Are the Subunits of DNA and RNA
50
50
Macromolecules in Cells
Each Macromolecule Contains a Specific
Sequence of Subunits
Noncovalent Bonds Specify the Precise Shape
of a Macromolecule
Noncovalent Bonds Allow a Macromolecule
to Bind Other Selected Molecules
58
Essential Concepts
64
Questions
80
41
44
45
46
46
47
48
49
51
52
53
55
56
59
62
63
xiv
Detailed Contents
Chapter 3
Energy, Catalysis, and Biosynthesis
The Use of Energy by Cells
Biological Order Is Made Possible by the
Release of Heat Energy from Cells
Cells Can Convert Energy from One Form to
Another
Photosynthetic Organisms Use Sunlight to
Synthesize Organic Molecules
Cells Obtain Energy by the Oxidation of
Organic Molecules
Oxidation and Reduction Involve Electron
Transfers
83
84
84
86
87
88
89
Free Energy and Catalysis
90
Chemical Reactions Proceed in the Direction
that Causes a Loss of Free Energy
91
Enzymes Reduce the Energy Needed to Initiate
Spontaneous Reactions
91
The Free-Energy Change for a Reaction
Determines Whether It Can Occur
93
ΔG Changes As a Reaction Proceeds Toward
Equilibrium
94
The Standard Free-Energy Change, ΔG°, Makes
it Possible to Compare the Energetics of
Different Reactions
94
The Equilibrium Constant Is Directly Proportional
to ΔG°
95
In Complex Reactions, the Equilibrium Constant
Includes the Concentrations of All Reactants
and Products
98
The Equilibrium Constant Indicates the
Strength of Molecular Interactions
98
For Sequential Reactions, the Changes in
Free Energy Are Additive
99
Thermal Motion Allows Enzymes to Find Their
Substrates
100
Vmax and KM Measure Enzyme Performance
102
Activated Carriers and Biosynthesis
The Formation of an Activated Carrier Is
Coupled to an Energetically Favorable
Reaction
ATP Is the Most Widely Used Activated Carrier
Energy Stored in ATP Is Often Harnessed to
Join Two Molecules Together
NADH and NADPH Are Both Activated
Carriers of Electrons
NADPH and NADH Have Different Roles in Cells
Cells Make Use of Many Other Activated
Carriers
The Synthesis of Biological Polymers Requires
an Energy Input
103
Essential Concepts
116
Questions
117
103
107
109
109
110
111
113
Chapter 4
Protein Structure and Function
121
The Shape and Structure of Proteins
The Shape of a Protein Is Specified by Its Amino
Acid Sequence
Proteins Fold into a Conformation of Lowest
Energy
Proteins Come in a Wide Variety of Complicated
Shapes
The α Helix and the β Sheet Are Common
Folding Patterns
Helices Form Readily in Biological Structures
β Sheets Form Rigid Structures at the Core
of Many Proteins
Proteins Have Several Levels of Organization
Many Proteins Also Contain Unstructured
Regions
Few of the Many Possible Polypeptide Chains
Will Be Useful
Proteins Can Be Classified into Families
Large Protein Molecules Often Contain More
Than One Polypeptide Chain
Proteins Can Assemble into Filaments, Sheets,
or Spheres
Some Types of Proteins Have Elongated Fibrous
Shapes
Extracellular Proteins Are Often Stabilized by
Covalent Cross-Linkages
123
How Proteins Work
All Proteins Bind to Other Molecules
There Are Billions of Different Antibodies,
Each with a Different Binding Site
Enzymes Are Powerful and Highly Specific
Catalysts
Lysozyme Illustrates How an Enzyme Works
Many Drugs Inhibit Enzymes
Tightly Bound Small Molecules Add Extra
Functions to Proteins
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How Proteins Are Controlled
The Catalytic Activities of Enzymes Are Often
Regulated by Other Molecules
Allosteric Enzymes Have Two or More Binding
Sites That Influence One Another
Phosphorylation Can Control Protein Activity
by Causing a Conformational Change
Covalent Modifications Also Control the
Location and Interaction of Proteins
GTP-Binding Proteins Are Also Regulated by the
Cyclic Gain and Loss of a Phosphate Group
ATP Hydrolysis Allows Motor Proteins to
Produce Directed Movements in Cells
Proteins Often Form Large Complexes That
Function as Protein Machines
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How Proteins Are Studied
Proteins Can be Purified from Cells or Tissues
Determining a Protein’s Structure Begins with
Determining Its Amino Acid Sequence
Genetic Engineering Techniques Permit the
Large-Scale Production, Design, and Analysis
of Almost Any Protein
The Relatedness of Proteins Aids the Prediction
of Protein Structure and Function
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Essential Concepts
168
Questions
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Chapter 5 DNA and Chromosomes
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The Structure of DNA
172
A DNA Molecule Consists of Two Complementary
Chains of Nucleotides
173
The Structure of DNA Provides a Mechanism
for Heredity
178
The Structure of Eukaryotic
Chromosomes
Eukaryotic DNA Is Packaged into Multiple
Chromosomes
Chromosomes Contain Long Strings of Genes
Specialized DNA Sequences Are Required for
DNA Replication and Chromosome
Segregation
Interphase Chromosomes Are Not Randomly
Distributed Within the Nucleus
The DNA in Chromosomes Is Always Highly
Condensed
Nucleosomes Are the Basic Units of Eukaryotic
Chromosome Structure
Chromosome Packing Occurs on Multiple Levels
The Regulation of Chromosome
Structure
Changes in Nucleosome Structure Allow
Access to DNA
Interphase Chromosomes Contain Both
Condensed and More Extended Forms
of Chromatin
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Essential Concepts
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Questions
193
Chapter 6 DNA Replication, Repair,
and Recombination
DNA Replication
Base-Pairing Enables DNA Replication
DNA Synthesis Begins at Replication Origins
Two Replication Forks Form at Each Replication
Origin
DNA Polymerase Synthesizes DNA Using a
Parental Strand as Template
The Replication Fork Is Asymmetrical
DNA Polymerase Is Self-correcting
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Short Lengths of RNA Act as Primers for
DNA Synthesis
Proteins at a Replication Fork Cooperate to
Form a Replication Machine
Telomerase Replicates the Ends of Eukaryotic
Chromosomes
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DNA Repair
DNA Damage Occurs Continually in Cells
Cells Possess a Variety of Mechanisms for
Repairing DNA
A DNA Mismatch Repair System Removes
Replication Errors That Escape Proofreading
Double-Strand DNA Breaks Require a Different
Strategy for Repair
Homologous Recombination Can Flawlessly
Repair DNA Double-Strand Breaks
Failure to Repair DNA Damage Can Have Severe
Consequences for a Cell or Organism
A Record of the Fidelity of DNA Replication and
Repair Is Preserved in Genome Sequences
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Essential Concepts
220
Questions
221
Chapter 7 From DNA to Protein:
How Cells Read the Genome
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From DNA to RNA
Portions of DNA Sequence Are Transcribed
into RNA
Transcription Produces RNA That Is
Complementary to One Strand of DNA
Cells Produce Various Types of RNA
Signals in DNA Tell RNA Polymerase Where
to Start and Finish Transcription
Initiation of Eukaryotic Gene Transcription
Is a Complex Process
Eukaryotic RNA Polymerase Requires General
Transcription Factors
Eukaryotic mRNAs Are Processed in the Nucleus
In Eukaryotes, Protein-Coding Genes Are
Interrupted by Noncoding Sequences
Called Introns
Introns Are Removed From Pre-mRNAs by
RNA Splicing
Mature Eukaryotic mRNAs Are Exported
from the Nucleus
mRNA Molecules Are Eventually Degraded
in the Cytosol
The Earliest Cells May Have Had Introns in
Their Genes
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From RNA to Protein
An mRNA Sequence Is Decoded in Sets of
Three Nucleotides
tRNA Molecules Match Amino Acids to
Codons in mRNA
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Detailed Contents
Specific Enzymes Couple tRNAs to the Correct
Amino Acid
The mRNA Message Is Decoded by Ribosomes
The Ribosome Is a Ribozyme
Specific Codons in mRNA Signal the Ribosome
Where to Start and to Stop Protein Synthesis
Proteins Are Made on Polyribosomes
Inhibitors of Prokaryotic Protein Synthesis Are
Used as Antibiotics
Controlled Protein Breakdown Helps Regulate
the Amount of Each Protein in a Cell
There Are Many Steps Between DNA and
Protein
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Specialized Cell Types Can Be Experimentally
Reprogrammed to Become Pluripotent
Stem Cells
The Formation of an Entire Organ Can Be
Triggered by a Single Transcription Regulator
Epigenetic Mechanisms Allow Differentiated
Cells to Maintain Their Identity
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RNA and the Origins of Life
Life Requires Autocatalysis
RNA Can Both Store Information and Catalyze
Chemical Reactions
RNA Is Thought to Predate DNA in Evolution
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Post-Transcriptional Controls
Each mRNA Controls Its Own Degradation and
Translation
Regulatory RNAs Control the Expression of
Thousands of Genes
MicroRNAs Direct the Destruction of Target
mRNAs
Small Interfering RNAs Are Produced From
Double-Stranded, Foreign RNAs to Protect
Cells From Infections
Thousands of Long Noncoding RNAs May Also
Regulate Mammalian Gene Activity
Essential Concepts
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Essential Concepts
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Questions
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Questions
286
Chapter 8 Control of Gene Expression
261
An Overview of Gene Expression
The Different Cell Types of a Multicellular
Organism Contain the Same DNA
Different Cell Types Produce Different Sets
of Proteins
A Cell Can Change the Expression of Its Genes
in Response to External Signals
Gene Expression Can Be Regulated at Various
Steps from DNA to RNA to Protein
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Chapter 9 How Genes and Genomes
Evolve
289
How Transcriptional Switches Work
Transcription Regulators Bind to Regulatory
DNA Sequences
Transcriptional Switches Allow Cells to Respond
to Changes in Their Environment
Repressors Turn Genes Off and Activators
Turn Them On
An Activator and a Repressor Control the Lac
Operon
Eukaryotic Transcription Regulators Control
Gene Expression from a Distance
Eukaryotic Transcription Regulators Help
Initiate Transcription by Recruiting
Chromatin-Modifying Proteins
265
The Molecular Mechanisms That
Create Specialized Cell Types
Eukaryotic Genes Are Controlled by
Combinations of Transcription Regulators
The Expression of Different Genes Can Be
Coordinated by a Single Protein
Combinatorial Control Can Also Generate
Different Cell Types
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Generating Genetic Variation
In Sexually Reproducing Organisms, Only
Changes to the Germ Line Are Passed
On To Progeny
Point Mutations Are Caused by Failures of the
Normal Mechanisms for Copying and
Repairing DNA
Point Mutations Can Change the Regulation
of a Gene
DNA Duplications Give Rise to Families of
Related Genes
The Evolution of the Globin Gene Family
Shows How Gene Duplication and Divergence
Can Produce New Proteins
Whole-Genome Duplications Have Shaped the
Evolutionary History of Many Species
Novel Genes Can Be Created by Exon
Shuffling
The Evolution of Genomes Has Been
Profoundly Influenced by the Movement
of Mobile Genetic Elements
Genes Can Be Exchanged Between Organisms
by Horizontal Gene Transfer
290
Reconstructing Life’s Family Tree
Genetic Changes That Provide a Selective
Advantage Are Likely to Be Preserved
Closely Related Organisms Have Genomes
That Are Similar in Organization As Well
As Sequence
Functionally Important Genome Regions
Show Up As Islands of Conserved DNA
Sequence
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Detailed Contents
Genome Comparisons Show That Vertebrate
Genomes Gain and Lose DNA Rapidly
Sequence Conservation Allows Us to Trace
Even the Most Distant Evolutionary
Relationships
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TRANSPOSONS AND VIRUSES
Mobile Genetic Elements Encode the
Components They Need for Movement
The Human Genome Contains Two Major
Families of Transposable Sequences
Viruses Can Move Between Cells and Organisms
Retroviruses Reverse the Normal Flow of
Genetic Information
307
Examining the Human Genome
The Nucleotide Sequences of Human Genomes
Show How Our Genes Are Arranged
Accelerated Changes in Conserved Genome
Sequences Help Reveal What Makes Us
Human
Genome Variation Contributes to Our
Individuality—But How?
Differences in Gene Regulation May Help
Explain How Animals With Similar Genomes
Can Be So Different
311
Essential Concepts
321
Questions
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Chapter 10
Modern Recombinant DNA Technology
325
Manipulating and Analyzing DNA
Molecules
Restriction Nucleases Cut DNA Molecules
at Specific Sites
Gel Electrophoresis Separates DNA Fragments
of Different Sizes
Bands of DNA in a Gel Can Be Visualized Using
Fluorescent Dyes or Radioisotopes
Hybridization Provides a Sensitive Way to
Detect Specific Nucleotide Sequences
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DNA Cloning IN BACTERIA
DNA Cloning Begins with Genome
Fragmentation and Production of
Recombinant DNAs
Recombinant DNA Can Be Inserted Into
Plasmid Vectors
Recombinant DNA Can Be Copied Inside
Bacterial Cells
Genes Can Be Isolated from a DNA Library
cDNA Libraries Represent the mRNAs Produced
by Particular Cells
330
DNA Cloning by PCR
PCR Uses a DNA Polymerase to Amplify
Selected DNA Sequences in a Test Tube
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Multiple Cycles of Amplification In Vitro
Generate Billions of Copies of the Desired
Nucleotide Sequence
PCR is Also Used for Diagnostic and Forensic
Applications
Exploring and Exploiting Gene
function
Whole Genomes Can Be Sequenced Rapidly
Next-Generation Sequencing Techniques Make
Genome Sequencing Faster and Cheaper
Comparative Genome Analyses Can Identify
Genes and Predict Their Function
Analysis of mRNAs By Microarray or RNA-Seq
Provides a Snapshot of Gene Expression
In Situ Hybridization Can Reveal When and
Where a Gene Is Expressed
Reporter Genes Allow Specific Proteins to be
Tracked in Living Cells
The Study of Mutants Can Help Reveal the
Function of a Gene
RNA Interference (RNAi) Inhibits the Activity
of Specific Genes
A Known Gene Can Be Deleted or Replaced
With an Altered Version
Mutant Organisms Provide Useful Models
of Human Disease
Transgenic Plants Are Important for Both
Cell Biology and Agriculture
Even Rare Proteins Can Be Made in Large
Amounts Using Cloned DNA
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Essential Concepts
355
Questions
356
Chapter 11
Membrane Structure
359
The Lipid Bilayer
Membrane Lipids Form Bilayers in Water
The Lipid Bilayer Is a Flexible Two-dimensional
Fluid
The Fluidity of a Lipid Bilayer Depends on Its
Composition
Membrane Assembly Begins in the ER
Certain Phospholipids Are Confined to One
Side of the Membrane
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Membrane Proteins
Membrane Proteins Associate with the Lipid
Bilayer in Different Ways
A Polypeptide Chain Usually Crosses the
Lipid Bilayer as an α Helix
Membrane Proteins Can Be Solubilized in
Detergents
We Know the Complete Structure of
Relatively Few Membrane Proteins
The Plasma Membrane Is Reinforced by the
Underlying Cell Cortex
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Detailed Contents
A Cell Can Restrict the Movement of Its
Membrane Proteins
The Cell Surface Is Coated with Carbohydrate
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Essential Concepts
Questions
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381
Chapter 12
Transport Across Cell Membranes
383
Principles of TRANSMembrane
Transport
Lipid Bilayers Are Impermeable to Ions and
Most Uncharged Polar Molecules
The Ion Concentrations Inside a Cell Are Very
Different from Those Outside
Differences in the Concentration of Inorganic
Ions Across a Cell Membrane Create a
Membrane Potential
Cells Contain Two Classes of Membrane
Transport Proteins: Transporters and Channels
Solutes Cross Membranes by Either Passive
or Active Transport
Both the Concentration Gradient and Membrane
Potential Influence the Passive Transport of
Charged Solutes
Water Moves Passively Across Cell Membranes
Down Its Concentration Gradient—a Process
Called Osmosis
Transporters and Their Functions
Passive Transporters Move a Solute Along Its
Electrochemical Gradient
Pumps Actively Transport a Solute Against Its
Electrochemical Gradient
The Na+ Pump in Animal Cells Uses Energy
Supplied by ATP to Expel Na+ and Bring
in K+
The Na+ Pump Generates a Steep
Concentration Gradient of Na+ Across the
Plasma Membrane
Ca2+ Pumps Keep the Cytosolic Ca2+
Concentration Low
Coupled Pumps Exploit Solute Gradients to
Mediate Active Transport
The Electrochemical Na+ Gradient Drives
Coupled Pumps in the Plasma Membrane
of Animal Cells
Electrochemical H+ Gradients Drive Coupled
Pumps in Plants, Fungi, and Bacteria
Ion Channels and the Membrane
Potential
Ion Channels Are Ion-selective and Gated
Membrane Potential Is Governed by the
Permeability of a Membrane to Specific Ions
Ion Channels Randomly Snap Between Open
and Closed States
Different Types of Stimuli Influence the
Opening and Closing of Ion Channels
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Voltage-gated Ion Channels Respond to the
Membrane Potential
Ion Channels and Nerve Cell
Signaling
Action Potentials Allow Rapid Long-Distance
Communication Along Axons
Action Potentials Are Mediated by Voltagegated Cation Channels
Voltage-gated Ca2+ Channels in Nerve
Terminals Convert an Electrical Signal
into a Chemical Signal
Transmitter-gated Ion Channels in the
Postsynaptic Membrane Convert the
Chemical Signal Back into an Electrical Signal
Neurotransmitters Can Be Excitatory or
Inhibitory
Most Psychoactive Drugs Affect Synaptic
Signaling by Binding to Neurotransmitter
Receptors
The Complexity of Synaptic Signaling Enables
Us to Think, Act, Learn, and Remember
Optogenetics Uses Light-gated Ion Channels
to Transiently Activate or Inactivate Neurons
in Living Animals
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Essential Concepts
415
Questions
417
Chapter 13
How Cells Obtain Energy From Food
419
The Breakdown and Utilization of
Sugars and Fats
Food Molecules Are Broken Down in
Three Stages
Glycolysis Extracts Energy from the Splitting
of Sugar
Glycolysis Produces Both ATP and NADH
Fermentations Can Produce ATP in the
Absence of Oxygen
Glycolytic Enzymes Couple Oxidation to Energy
Storage in Activated Carriers
Several Organic Molecules Are Converted
to Acetyl CoA in the Mitochondrial Matrix
The Citric Acid Cycle Generates NADH by
Oxidizing Acetyl Groups to CO2
Many Biosynthetic Pathways Begin with
Glycolysis or the Citric Acid Cycle
Electron Transport Drives the Synthesis of the
Majority of the ATP in Most Cells
Regulation of Metabolism
Catabolic and Anabolic Reactions Are
Organized and Regulated
Feedback Regulation Allows Cells to Switch from
Glucose Breakdown to Glucose Synthesis
Cells Store Food Molecules in Special Reservoirs
to Prepare for Periods of Need
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Detailed Contents
Essential Concepts
445
Questions
446
Chapter 14
Energy Generation in Mitochondria
and Chloroplasts
Cells Obtain Most of Their Energy by a
Membrane-based Mechanism
Chemiosmotic Coupling is an Ancient Process,
Preserved in Present-Day Cells
Mitochondria and Oxidative
Phosphorylation
Mitochondria Can Change Their Shape,
Location, and Number to Suit a Cell’s Needs
A Mitochondrion Contains an Outer Membrane,
an Inner Membrane, and Two Internal
Compartments
The Citric Acid Cycle Generates the High-Energy
Electrons Required for ATP Production
The Movement of Electrons is Coupled to the
Pumping of Protons
Protons Are Pumped Across the Inner
Mitochondrial Membrane by Proteins in the
Electron-Transport Chain
Proton Pumping Produces a Steep
Electrochemical Proton Gradient Across the
Inner Mitochondrial Membrane
ATP Synthase Uses the Energy Stored in the
Electrochemical Proton Gradient to Produce
ATP
Coupled Transport Across the Inner
Mitochondrial Membrane Is Also Driven by
the Electrochemical Proton Gradient
The Rapid Conversion of ADP to ATP in
Mitochondria Maintains a High ATP/ADP
Ratio in Cells
Cell Respiration Is Amazingly Efficient
Molecular Mechanisms of Electron
Transport and Proton Pumping
Protons Are Readily Moved by the Transfer of
Electrons
The Redox Potential Is a Measure of Electron
Affinities
Electron Transfers Release Large Amounts
of Energy
Metals Tightly Bound to Proteins Form Versatile
Electron Carriers
Cytochrome c Oxidase Catalyzes the Reduction
of Molecular Oxygen
Chloroplasts and Photosynthesis
Chloroplasts Resemble Mitochondria but Have
an Extra Compartment—the Thylakoid
Photosynthesis Generates—Then Consumes—
ATP and NADPH
Chlorophyll Molecules Absorb the Energy of
Sunlight
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Excited Chlorophyll Molecules Funnel Energy
into a Reaction Center
A Pair of Photosystems Cooperate to Generate
Both ATP and NADPH
Oxygen Is Generated by a Water-Splitting
Complex Associated with Photosystem II
The Special Pair in Photosystem I Receives its
Electrons from Photosystem II
Carbon Fixation Uses ATP and NADPH to
Convert CO2 into Sugars
Sugars Generated by Carbon Fixation Can Be
Stored As Starch or Consumed to Produce
ATP
The EVOLUTION OF ENERGY-GENERATING
SYSTEMS
Oxidative Phosphorylation Evolved in Stages
Photosynthetic Bacteria Made Even Fewer
Demands on Their Environment
The Lifestyle of Methanococcus Suggests That
Chemiosmotic Coupling Is an Ancient Process
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481
Essential Concepts
482
Questions
483
Chapter 15
Intracellular Compartments and
Protein Transport
487
Membrane-enclosed Organelles
Eukaryotic Cells Contain a Basic Set of
Membrane-enclosed Organelles
Membrane-enclosed Organelles Evolved in
Different Ways
488
Protein Sorting
Proteins Are Transported into Organelles by
Three Mechanisms
Signal Sequences Direct Proteins to the Correct
Compartment
Proteins Enter the Nucleus Through Nuclear
Pores
Proteins Unfold to Enter Mitochondria and
Chloroplasts
Proteins Enter Peroxisomes from Both the
Cytosol and the Endoplasmic Reticulum
Proteins Enter the Endoplasmic Reticulum
While Being Synthesized
Soluble Proteins Made on the ER Are Released
into the ER Lumen
Start and Stop Signals Determine the
Arrangement of a Transmembrane Protein
in the Lipid Bilayer
492
Vesicular Transport
Transport Vesicles Carry Soluble Proteins and
Membrane Between Compartments
Vesicle Budding Is Driven by the Assembly of a
Protein Coat
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Detailed Contents
Vesicle Docking Depends on Tethers and
SNAREs
505
Secretory Pathways
Most Proteins Are Covalently Modified in the ER
Exit from the ER Is Controlled to Ensure Protein
Quality
The Size of the ER Is Controlled by the Demand
for Protein
Proteins Are Further Modified and Sorted in
the Golgi Apparatus
Secretory Proteins Are Released from the Cell
by Exocytosis
507
507
Endocytic Pathways
Specialized Phagocytic Cells Ingest Large
Particles
Fluid and Macromolecules Are Taken Up by
Pinocytosis
Receptor-mediated Endocytosis Provides a
Specific Route into Animal Cells
Endocytosed Macromolecules Are Sorted in
Endosomes
Lysosomes Are the Principal Sites of
Intracellular Digestion
515
Essential Concepts
Questions
Chapter 16
Cell Signaling
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511
Many G Proteins Activate Membrane-bound
Enzymes that Produce Small Messenger
Molecules
The Cyclic AMP Signaling Pathway Can Activate
Enzymes and Turn On Genes
The Inositol Phospholipid Pathway Triggers a
Rise in Intracellular Ca2+
A Ca2+ Signal Triggers Many Biological
Processes
GPCR-Triggered Intracellular Signaling
Cascades Can Achieve Astonishing Speed,
Sensitivity, and Adaptability
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520
Enzyme-coupled Receptors
Activated RTKs Recruit a Complex of
Intracellular Signaling Proteins
Most RTKs Activate the Monomeric GTPase
Ras
RTKs Activate PI 3-Kinase to Produce Lipid
Docking Sites in the Plasma Membrane
Some Receptors Activate a Fast Track to
the Nucleus
Cell–Cell Communication Evolved
Independently in Plants and Animals
Protein Kinase Networks Integrate Information
to Control Complex Cell Behaviors
522
Essential Concepts
561
Questions
563
Chapter 17
Cytoskeleton
565
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516
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525
General Principles of Cell Signaling
Signals Can Act over a Long or Short Range
Each Cell Responds to a Limited Set of
Extracellular Signals, Depending on Its
History and Its Current State
A Cell’s Response to a Signal Can Be Fast
or Slow
Some Hormones Cross the Plasma Membrane
and Bind to Intracellular Receptors
Some Dissolved Gases Cross the Plasma
Membrane and Activate Intracellular
Enzymes Directly
Cell-Surface Receptors Relay Extracellular
Signals via Intracellular Signaling Pathways
Some Intracellular Signaling Proteins Act as
Molecular Switches
Cell-Surface Receptors Fall into Three Main
Classes
Ion-channel–coupled Receptors Convert
Chemical Signals into Electrical Ones
526
526
G-protein-coupled Receptors
Stimulation of GPCRs Activates G-Protein
Subunits
Some Bacterial Toxins Cause Disease by
Altering the Activity of G Proteins
Some G Proteins Directly Regulate Ion Channels
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560
Intermediate Filaments
Intermediate Filaments Are Strong and Ropelike
Intermediate Filaments Strengthen Cells
Against Mechanical Stress
The Nuclear Envelope Is Supported by a
Meshwork of Intermediate Filaments
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567
Microtubules
Microtubules Are Hollow Tubes with
Structurally Distinct Ends
The Centrosome Is the Major Microtubuleorganizing Center in Animal Cells
Growing Microtubules Display Dynamic
Instability
Dynamic Instability is Driven by GTP Hydrolysis
Microtubule Dynamics Can be Modified by
Drugs
Microtubules Organize the Cell Interior
Motor Proteins Drive Intracellular Transport
Microtubules and Motor Proteins Position
Organelles in the Cytoplasm
Cilia and Flagella Contain Stable Microtubules
Moved by Dynein
571
Actin Filaments
Actin Filaments Are Thin and Flexible
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Detailed Contents
Actin and Tubulin Polymerize by Similar
Mechanisms
Many Proteins Bind to Actin and Modify
Its Properties
A Cortex Rich in Actin Filaments Underlies the
Plasma Membrane of Most Eukaryotic Cells
Cell Crawling Depends on Cortical Actin
Actin Associates with Myosin to Form
Contractile Structures
Extracellular Signals Can Alter the Arrangement
of Actin Filaments
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591
591
Muscle Contraction
Muscle Contraction Depends on Interacting
Filaments of Actin and Myosin
Actin Filaments Slide Against Myosin Filaments
During Muscle Contraction
Muscle Contraction Is Triggered by a Sudden
Rise in Cytosolic Ca2+
Different Types of Muscle Cells Perform
Different Functions
592
Essential Concepts
Questions
599
600
Chapter 18
The Cell-Division Cycle
603
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598
Overview of the Cell Cycle
The Eukaryotic Cell Cycle Usually Includes Four
Phases
A Cell-Cycle Control System Triggers the Major
Processes of the Cell Cycle
Cell-Cycle Control is Similar in All Eukaryotes
604
The Cell-Cycle Control System
The Cell-Cycle Control System Depends on
Cyclically Activated Protein Kinases called
Cdks
Different Cyclin–Cdk Complexes Trigger
Different Steps in the Cell Cycle
Cyclin Concentrations are Regulated by
Transcription and by Proteolysis
The Activity of Cyclin–Cdk Complexes Depends
on Phosphorylation and Dephosphorylation
Cdk Activity Can be Blocked by Cdk Inhibitor
Proteins
The Cell-Cycle Control System Can Pause the
Cycle in Various Ways
607
G1 PHASE
Cdks are Stably Inactivated in G1
Mitogens Promote the Production of the Cyclins
that Stimulate Cell Division
DNA Damage Can Temporarily Halt Progression
Through G1
Cells Can Delay Division for Prolonged Periods
by Entering Specialized Nondividing States
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614
S Phase
605
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615
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616
S-Cdk Initiates DNA Replication and Blocks
Re-Replication
Incomplete Replication Can Arrest the Cell
Cycle in G2
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618
M Phase
M-Cdk Drives Entry Into M Phase and Mitosis
Cohesins and Condensins Help Configure
Duplicated Chromosomes for Separation
Different Cytoskeletal Assemblies Carry
Out Mitosis and Cytokinesis
M Phase Occurs in Stages
618
618
Mitosis
Centrosomes Duplicate To Help Form the
Two Poles of the Mitotic Spindle
The Mitotic Spindle Starts to Assemble in
Prophase
Chromosomes Attach to the Mitotic Spindle
at Prometaphase
Chromosomes Assist in the Assembly of the
Mitotic Spindle
Chromosomes Line Up at the Spindle Equator
at Metaphase
Proteolysis Triggers Sister-Chromatid Separation
at Anaphase
Chromosomes Segregate During Anaphase
An Unattached Chromosome Will Prevent
Sister-Chromatid Separation
The Nuclear Envelope Re-forms at Telophase
621
Cytokinesis
The Mitotic Spindle Determines the Plane of
Cytoplasmic Cleavage
The Contractile Ring of Animal Cells Is Made
of Actin and Myosin Filaments
Cytokinesis in Plant Cells Involves the
Formation of a New Cell Wall
Membrane-Enclosed Organelles Must Be
Distributed to Daughter Cells When a
Cell Divides
630
Control of Cell NumberS and Cell Size
Apoptosis Helps Regulate Animal Cell Numbers
Apoptosis Is Mediated by an Intracellular
Proteolytic Cascade
The Intrinsic Apoptotic Death Program Is
Regulated by the Bcl2 Family of Intracellular
Proteins
Extracellular Signals Can Also Induce Apoptosis
Animal Cells Require Extracellular Signals
to Survive, Grow, and Divide
Survival Factors Suppress Apoptosis
Mitogens Stimulate Cell Division by Promoting
Entry into S Phase
Growth Factors Stimulate Cells to Grow
Some Extracellular Signal Proteins Inhibit
Cell Survival, Division, or Growth
633
634
619
619
620
621
624
624
626
626
627
627
629
629
630
631
632
632
634
636
637
637
638
639
639
640
xxii
Detailed Contents
Essential Concepts
641
Questions
643
Chapter 19
Sexual Reproduction and the Power
of Genetics
645
The Benefits of Sex
Sexual Reproduction Involves Both Diploid and
Haploid Cells
Sexual Reproduction Generates Genetic
Diversity
Sexual Reproduction Gives Organisms a
Competitive Advantage in a Changing
Environment
646
Meiosis and Fertilization
Meiosis Involves One Round of DNA Replication
Followed by Two Rounds of Cell Division
Meiosis Requires the Pairing of Duplicated
Homologous Chromosomes
Crossing-Over Occurs Between the Duplicated
Maternal and Paternal Chromosomes in Each
Bivalent
Chromosome Pairing and Crossing-Over
Ensure the Proper Segregation of Homologs
The Second Meiotic Division Produces Haploid
Daughter Cells
Haploid Gametes Contain Reassorted Genetic
Information
Meiosis Is Not Flawless
Fertilization Reconstitutes a Complete Diploid
Genome
648
Mendel and the Laws of Inheritance
Mendel Studied Traits That Are Inherited in
a Discrete Fashion
Mendel Disproved the Alternative Theories
of Inheritance
Mendel’s Experiments Revealed the Existence
of Dominant and Recessive Alleles
Each Gamete Carries a Single Allele for Each
Character
Mendel’s Law of Segregation Applies to All
Sexually Reproducing Organisms
Alleles for Different Traits Segregate
Independently
The Behavior of Chromosomes During Meiosis
Underlies Mendel’s Laws of Inheritance
Even Genes on the Same Chromosome Can
Segregate Independently by Crossing-Over
Mutations in Genes Can Cause a Loss of
Function or a Gain of Function
Each of Us Carries Many Potentially Harmful
Recessive Mutations
657
Genetics as an Experimental Tool
The Classical Genetic Approach Begins with
Random Mutagenesis
667
646
647
648
Genetic Screens Identify Mutants Deficient
in Specific Cell Processes
Conditional Mutants Permit the Study of Lethal
Mutations
A Complementation Test Reveals Whether Two
Mutations Are in the Same Gene
Rapid and Cheap DNA Sequencing Has
Revolutionized Human Genetic Studies
Linked Blocks of Polymorphisms Have Been
Passed Down from Our Ancestors
Our Genome Sequences Provide Clues to our
Evolutionary History
Polymorphisms Can Aid the Search for Mutations
Associated with Disease
Genomics Is Accelerating the Discovery of
Rare Mutations that Predispose Us to
Serious Disease
668
670
671
672
672
673
674
675
649
Essential Concepts
678
651
Questions
679
652
Chapter 20
Cell Communities: Tissues, Stem Cells,
and Cancer
683
653
654
654
656
657
658
658
659
660
661
662
664
664
665
666
667
Extracellular Matrix and Connective
Tissues
Plant Cells Have Tough External Walls
Cellulose Microfibrils Give the Plant Cell Wall
Its Tensile Strength
Animal Connective Tissues Consist Largely of
Extracellular Matrix
Collagen Provides Tensile Strength in Animal
Connective Tissues
Cells Organize the Collagen That They Secrete
Integrins Couple the Matrix Outside a Cell to
the Cytoskeleton Inside It
Gels of Polysaccharides and Proteins Fill
Spaces and Resist Compression
684
685
686
688
688
690
691
692
Epithelial Sheets and Cell Junctions
Epithelial Sheets Are Polarized and Rest on a
Basal Lamina
Tight Junctions Make an Epithelium Leakproof and Separate Its Apical and Basal
Surfaces
Cytoskeleton-linked Junctions Bind Epithelial
Cells Robustly to One Another and to the
Basal Lamina
Gap Junctions Allow Cytosolic Inorganic Ions
and Small Molecules to Pass from Cell to Cell
694
Tissue Maintenance and Renewal
Tissues Are Organized Mixtures of Many
Cell Types
Different Tissues Are Renewed at Different
Rates
Stem Cells Generate a Continuous Supply
of Terminally Differentiated Cells
702
695
696
697
700
703
705
705
Detailed Contents
Specific Signals Maintain Stem-Cell Populations
Stem Cells Can Be Used to Repair Lost or
Damaged Tissues
Therapeutic Cloning and Reproductive Cloning
Are Very Different Enterprises
Induced Pluripotent Stem Cells Provide a
Convenient Source of Human ES-like Cells
707
Cancer
Cancer Cells Proliferate, Invade, and Metastasize
Epidemiological Studies Identify Preventable
Causes of Cancer
Cancers Develop by an Accumulation of
Mutations
Cancer Cells Evolve, Giving Them an
Increasingly Competitive Advantage
Two Main Classes of Genes Are Critical for
Cancer: Oncogenes and Tumor Suppressor
Genes
Cancer-causing Mutations Cluster in a Few
Fundamental Pathways
Colorectal Cancer Illustrates How Loss of a
Tumor Suppressor Gene Can Lead to Cancer
An Understanding of Cancer Cell Biology
Opens the Way to New Treatments
712
712
Essential Concepts
724
Questions
726
708
710
711
713
714
715
717
719
719
720
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chapter ONE
1
Cells: The Fundamental Units
of Life
What does it mean to be living? Petunias, people, and pond scum are all
alive; stones, sand, and summer breezes are not. But what are the fundamental properties that characterize living things and distinguish them
from nonliving matter?
The answer begins with a basic fact that is taken for granted now, but
marked a revolution in thinking when first established 175 years ago.
All living things (or organisms) are built from cells: small, membraneenclosed units filled with a concentrated aqueous solution of chemicals
and endowed with the extraordinary ability to create copies of themselves by growing and then dividing in two. The simplest forms of life are
solitary cells. Higher organisms, including ourselves, are communities of
cells derived by growth and division from a single founder cell. Every animal or plant is a vast colony of individual cells, each of which performs
a specialized function that is regulated by intricate systems of cell-to-cell
communication.
Cells, therefore, are the fundamental units of life. Thus it is to cell biology—the study of cells and their structure, function, and behavior—that
we must look for an answer to the question of what life is and how it
works. With a deeper understanding of cells, we can begin to tackle the
grand historical problems of life on Earth: its mysterious origins, its stunning diversity produced by billions of years of evolution, and its invasion
of every conceivable habitat. At the same time, cell biology can provide
us with answers to the questions we have about ourselves: Where did we
come from? How do we develop from a single fertilized egg cell? How is
each of us similar to—yet different from—everyone else on Earth? Why do
we get sick, grow old, and die?
Unity and Diversity of
Cells
Cells Under the
Microscope
The Prokaryotic Cell
The Eukaryotic Cell
Model Organisms
2
Chapter 1
Cells: The Fundamental Units of Life
In this chapter, we begin by looking at the great variety of forms that cells
can show, and we take a preliminary glimpse at the chemical machinery
that all cells have in common. We then consider how cells are made visible under the microscope and what we see when we peer inside them.
Finally, we discuss how we can exploit the similarities of living things to
achieve a coherent understanding of all forms of life on Earth—from the
tiniest bacterium to the mightiest oak.
Unity and Diversity of Cells
Cell biologists often speak of “the cell” without specifying any particular cell. But cells are not all alike; in fact, they can be wildly different.
Biologists estimate that there may be up to 100 million distinct species
of living things on our planet. Before delving deeper into cell biology, we
must take stock: What does a bacterium have in common with a butterfly? What do the cells of a rose have in common with those of a dolphin?
And in what ways do the plethora of cell types within an individual multicellular organism differ?
Cells Vary Enormously in Appearance and Function
Let us begin with size. A bacterial cell—say a Lactobacillus in a piece of
cheese—is a few micrometers, or μm, in length. That’s about 25 times
smaller than the width of a human hair. A frog egg—which is also a single
cell—has a diameter of about 1 millimeter. If we scaled them up to make
the Lactobacillus the size of a person, the frog egg would be half a mile
high.
Cells vary just as widely in their shape (Figure 1–1). A typical nerve cell in
your brain, for example, is enormously extended; it sends out its electrical
signals along a fine protrusion that is 10,000 times longer than it is thick,
and it receives signals from other nerve cells through a mass of shorter
processes that sprout from its body like the branches of a tree (see Figure
1–1A). A Paramecium in a drop of pond water is shaped like a submarine
and is covered with thousands of cilia—hairlike extensions whose sinuous beating sweeps the cell forward, rotating as it goes (Figure 1–1B).
A cell in the surface layer of a plant is squat and immobile, surrounded
(A)
100 µm
(B)
25 µm
(C)
10 µm
(D)
5 µm
(E)
1 µm
Figure 1–1 Cells come in a variety of shapes and sizes. Note the very different scales of these micrographs. (A) Drawing of a single
nerve cell from a mammalian brain. This cell has a huge branching tree of processes, through which it receives signals from as many
as 100,000 other nerve cells. (B) Paramecium. This protozoan—a single giant cell—swims by means of the beating cilia that cover its
surface. (C) Chlamydomonas. This type of single-celled green algae is found all over the world—in soil, fresh water, oceans, and even
in the snow at the top of mountains. The cell makes its food like plants do—via photosynthesis—and it pulls itself through the water
using its paired flagella to do the breaststroke. (D) Saccharomyces cerevisiae. This yeast cell, used in baking bread, reproduces itself
by a process called budding. (E) Helicobacter pylori. This bacterium—a
causative agent of stomach ulcers—uses a handful of whiplike
ECB4 n1.100/1.01
flagella to propel itself through the stomach lining. (A, copyright Herederos de Santiago Ramón y Cajal, 1899; B, courtesy of Anne
Fleury, Michel Laurent, and André Adoutte; C, courtesy of Brian Piasecki; E, courtesy of Yutaka Tsutsumi.)
Unity and Diversity of Cells
by a rigid box of cellulose with an outer waterproof coating of wax. A
neutrophil or a macrophage in the body of an animal, by contrast, crawls
through tissues, constantly pouring itself into new shapes, as it searches
for and engulfs debris, foreign microorganisms, and dead or dying cells.
And so on.
Cells are also enormously diverse in their chemical requirements. Some
require oxygen to live; for others this gas is deadly. Some cells consume
little more than air, sunlight, and water as their raw materials; others
need a complex mixture of molecules produced by other cells.
These differences in size, shape, and chemical requirements often reflect
differences in cell function. Some cells are specialized factories for the
production of particular substances, such as hormones, starch, fat, latex,
or pigments. Others are engines, like muscle cells that burn fuel to do
mechanical work. Still others are electricity generators, like the modified
muscle cells in the electric eel.
Some modifications specialize a cell so much that they spoil its chances
of leaving any descendants. Such specialization would be senseless
for a cell that lived a solitary life. In a multicellular organism, however,
there is a division of labor among cells, allowing some cells to become
specialized to an extreme degree for particular tasks and leaving them
dependent on their fellow cells for many basic requirements. Even the
most basic need of all, that of passing on the genetic instructions of the
organism to the next generation, is delegated to specialists—the egg and
the sperm.
Question 1–1
“Life” is easy to recognize but
difficult to define. According to one
popular biology text, living things:
1. Are highly organized compared
to natural inanimate objects.
2. Display homeostasis, maintaining
a relatively constant internal
environment.
3. Reproduce themselves.
4. Grow and develop from simple
beginnings.
5. Take energy and matter from the
environment and transform it.
6. Respond to stimuli.
7. Show adaptation to their
environment.
Score a person, a vacuum cleaner,
and a potato with respect to these
characteristics.
Living Cells All Have a Similar Basic Chemistry
Despite the extraordinary diversity of plants and animals, people have
recognized from time immemorial that these organisms have something
in common, something that entitles them all to be called living things.
But while it seemed easy enough to recognize life, it was remarkably difficult to say in what sense all living things were alike. Textbooks had to
settle for defining life in abstract general terms related to growth, reproduction, and an ability to respond to the environment.
The discoveries of biochemists and molecular biologists have provided
an elegant solution to this awkward situation. Although the cells of all
living things are infinitely varied when viewed from the outside, they
are fundamentally similar inside. We now know that cells resemble one
another to an astonishing degree in the details of their chemistry. They are
composed of the same sorts of molecules, which participate in the same
types of chemical reactions (discussed in Chapter 2). In all organisms,
genetic information—in the form of genes—is carried in DNA molecules.
This information is written in the same chemical code, constructed out
of the same chemical building blocks, interpreted by essentially the same
chemical machinery, and replicated in the same way when an organism
reproduces. Thus, in every cell, the long DNA polymer chains are made
from the same set of four monomers, called nucleotides, strung together
in different sequences like the letters of an alphabet to convey information. In every cell, the information encoded in the DNA is read out, or
transcribed, into a chemically related set of polymers called RNA. A subset of these RNA molecules is in turn translated into yet another type of
polymer called a protein. This flow of information—from DNA to RNA
to protein—is so fundamental to life that it is referred to as the central
dogma (Figure 1–2).
The appearance and behavior of a cell are dictated largely by its
protein molecules, which serve as structural supports, chemical catalysts,
DNA synthesis
REPLICATION
DNA
nucleotides
RNA synthesis
TRANSCRIPTION
RNA
protein synthesis
TRANSLATION
PROTEIN
amino acids
Figure 1–2 In all living cells, genetic
information flows from DNA to RNA
(transcription) and from RNA to protein
(translation)—a sequence known as
the central dogma. The sequence of
nucleotides in a particular segment of
DNA (a gene)
transcribed into an RNA
ECB4 ise1.02/1.02
molecule, which can then be translated into
the linear sequence of amino acids of a
protein. Only a small part of the gene, RNA,
and protein are shown.
3
4
Chapter 1
(A)
Cells: The Fundamental Units of Life
(B)
Figure 1–3 All living organisms are
constructed from cells. A colony
of bacteria, a butterfly, a rose, and a
dolphin are all made of cells that have a
fundamentally similar chemistry and operate
according to the same basic principles.
(A, courtesy of Janice Carr; C, courtesy of
the John Innes Foundation; D, courtesy of
Jonathan Gordon, IFAW.)
(C)
(D)
molecular motors, and so on. Proteins are built from amino acids, and all
organisms use the same set of 20 amino acids to make their proteins.
But the amino acids are linked in different sequences, giving each type
ECB4 e1.03/1.03
of protein
molecule a different three-dimensional shape, or conformation, just as different sequences of letters spell different words. In this
way, the same basic biochemical machinery has served to generate the
whole gamut of life on Earth (Figure 1–3). A more detailed discussion
of the structure and function of proteins, RNA, and DNA is presented in
Chapters 4 through 8.
If cells are the fundamental unit of living matter, then nothing less than
a cell can truly be called living. Viruses, for example, are compact packages of genetic information—in the form of DNA or RNA—encased in
protein but they have no ability to reproduce themselves by their own
efforts. Instead, they get themselves copied by parasitizing the reproductive machinery of the cells that they invade. Thus, viruses are chemical
zombies: they are inert and inactive outside their host cells, but they can
exert a malign control over a cell once they gain entry.
All Present-Day Cells Have Apparently Evolved from the
Same Ancestral Cell
A cell reproduces by replicating its DNA and then dividing in two, passing
a copy of the genetic instructions encoded in its DNA to each of its daughter cells. That is why daughter cells resemble the parent cell. However,
the copying is not always perfect, and the instructions are occasionally
corrupted by mutations that change the DNA. For this reason, daughter
cells do not always match the parent cell exactly.
Mutations can create offspring that are changed for the worse (in that
they are less able to survive and reproduce), changed for the better (in
that they are better able to survive and reproduce), or changed in a neutral
way (in that they are genetically different but equally viable). The struggle
for survival eliminates the first, favors the second, and tolerates the third.
The genes of the next generation will be the genes of the survivors.
Question 1–2
Mutations are mistakes in the DNA
that change the genetic plan from
the previous generation. Imagine
a shoe factory. Would you expect
mistakes (i.e., unintentional changes)
in copying the shoe design to lead
to improvements in the shoes
produced? Explain your answer.
On occasion, the pattern of descent may be complicated by sexual reproduction, in which two cells of the same species fuse, pooling their DNA.
The genetic cards are then shuffled, re-dealt, and distributed in new combinations to the next generation, to be tested again for their ability to
promote survival and reproduction.
These simple principles of genetic change and selection, applied repeatedly over billions of cell generations, are the basis of evolution—the
process by which living species become gradually modified and adapted
to their environment in more and more sophisticated ways. Evolution
offers a startling but compelling explanation of why present-day cells
are so similar in their fundamentals: they have all inherited their genetic
instructions from the same common ancestor. It is estimated that this
ancestral cell existed between 3.5 and 3.8 billion years ago, and we must
Cells Under the Microscope
suppose that it contained a prototype of the universal machinery of all
life on Earth today. Through a very long process of mutation and natural
selection, the descendants of this ancestral cell have gradually diverged
to fill every habitat on Earth with organisms that exploit the potential of
the machinery in an endless variety of ways.
Genes Provide the Instructions for Cell Form, Function,
and Complex Behavior
A cell’s genome—that is, the entire sequence of nucleotides in an organism’s DNA—provides a genetic program that instructs the cell how to
behave. For the cells of plant and animal embryos, the genome directs
the growth and development of an adult organism with hundreds of different cell types. Within an individual plant or animal, these cells can be
extraordinarily varied, as we discuss in Chapter 20. Fat cells, skin cells,
bone cells, and nerve cells seem as dissimilar as any cells could be. Yet
all these differentiated cell types are generated during embryonic development from a single fertilized egg cell, and all contain identical copies of
the DNA of the species. Their varied characters stem from the way that
individual cells use their genetic instructions. Different cells express different genes: that is, they use their genes to produce some proteins and
not others, depending on their internal state and on cues that they and
their ancestor cells have received from their surroundings—mainly signals from other cells in the organism.
The DNA, therefore, is not just a shopping list specifying the molecules
that every cell must make, and a cell is not just an assembly of all the
items on the list. Each cell is capable of carrying out a variety of biological tasks, depending on its environment and its history, and it selectively
uses the information encoded in its DNA to guide its activities. Later in
this book, we will see in detail how DNA defines both the parts list of the
cell and the rules that decide when and where these parts are to be made.
Cells Under the Microscope
Today, we have the technology to decipher the underlying principles
that govern the structure and activity of the cell. But cell biology started
without these tools. The earliest cell biologists began by simply looking
at tissues and cells, and later breaking them open or slicing them up,
attempting to view their contents. What they saw was to them profoundly
baffling—a collection of tiny and scarcely visible objects whose relationship to the properties of living matter seemed an impenetrable mystery.
Nevertheless, this type of visual investigation was the first step toward
understanding cells, and it remains essential in the study of cell biology.
Cells were not made visible until the seventeenth century, when the
microscope was invented. For hundreds of years afterward, all that
was known about cells was discovered using this instrument. Light
microscopes use visible light to illuminate specimens, and they allowed
biologists to see for the first time the intricate structure that underpins all
living things.
Although these instruments now incorporate many sophisticated
improvements, the properties of light itself set a limit to the fineness of
detail they reveal. Electron microscopes, invented in the 1930s, go beyond
this limit by using beams of electrons instead of beams of light as the
source of illumination, greatly extending our ability to see the fine details
of cells and even making some of the larger molecules visible individually. These and other forms of microscopy remain vital tools in the
modern cell biology laboratory, where they continue to reveal new and
sometimes surprising details about the way cells are built and how they
operate.
5
6
Chapter 1
Cells: The Fundamental Units of Life
The Invention of the Light Microscope Led to the
Discovery of Cells
The development of the light microscope depended on advances in the
production of glass lenses. By the seventeenth century, lenses were powerful enough to make out details invisible to the naked eye. Using an
instrument equipped with such a lens, Robert Hooke examined a piece
of cork and in 1665 reported to the Royal Society of London that the cork
was composed of a mass of minute chambers. He called these chambers “cells,” based on their resemblance to the simple rooms occupied
by monks in a monastery. The name stuck, even though the structures
Hooke described were actually the cell walls that remained after the living
plant cells inside them had died. Later, Hooke and his Dutch contemporary Antoni van Leeuwenhoek were able to observe living cells, seeing
for the first time a world teeming with motile microscopic organisms.
For almost 200 years, such instruments—the first light microscopes—
remained exotic devices, available only to a few wealthy individuals. It
was not until the nineteenth century that microscopes began to be widely
used to look at cells. The emergence of cell biology as a distinct science
was a gradual process to which many individuals contributed, but its official birth is generally said to have been signaled by two publications: one
by the botanist Matthias Schleiden in 1838 and the other by the zoologist Theodor Schwann in 1839. In these papers, Schleiden and Schwann
documented the results of a systematic investigation of plant and animal
tissues with the light microscope, showing that cells were the universal
building blocks of all living tissues. Their work, and that of other nineteenth-century microscopists, slowly led to the realization that all living
cells are formed by the growth and division of existing cells—a principle
sometimes referred to as the cell theory (Figure 1–4). The implication that
(A)
(B)
50 µm
Figure 1–4 New cells form by growth and division of existing cells. (A) In 1880, Eduard Strasburger drew a living plant cell
(a hair cell from a Tradescantia flower), which he observed dividing into two daughter cells over a period of 2.5 hours. (B) A comparable
living plant cell photographed recently through a modern light microscope. (B, courtesy of Peter Hepler.)
ECB4 e1.04/1.04
Cells Under the Microscope
living organisms do not arise spontaneously but can be generated only
from existing organisms was hotly contested, but it was finally confirmed
in the 1860s by an elegant set of experiments performed by Louis Pasteur.
The principle that cells are generated only from preexisting cells and
inherit their characteristics from them underlies all of biology and gives
the subject a unique flavor: in biology, questions about the present are
inescapably linked to questions about the past. To understand why
present-day cells and organisms behave as they do, we need to understand their history, all the way back to the misty origins of the first cells
on Earth. Charles Darwin provided the key insight that makes this history comprehensible. His theory of evolution, published in 1859, explains
how random variation and natural selection gave rise to diversity among
organisms that share a common ancestry. When combined with the cell
theory, the theory of evolution leads us to view all life, from its beginnings
to the present day, as one vast family tree of individual cells. Although
this book is primarily about how cells work today, we will encounter the
theme of evolution again and again.
Light Microscopes Allow Examination of Cells and Some of
Their Components
If you cut a very thin slice from a suitable plant or animal tissue and view
it using a light microscope, you will see that the tissue is divided into
thousands of small cells. These may be either closely packed or separated
from one another by an extracellular matrix, a dense material often made
of protein fibers embedded in a polysaccharide gel (Figure 1–5). Each cell
is typically about 5–20 μm in diameter. If you have taken care of your
specimen so that its cells remain alive, you will be able to see particles
moving around inside individual cells. And if you watch patiently, you
may even see a cell slowly change shape and divide into two (see Figure
1–4 and a speeded-up video of cell division in a frog embryo in Movie 1.1).
Question 1–3
You have embarked on an ambitious
research project: to create life in a
test tube. You boil up a rich mixture
of yeast extract and amino acids
in a flask along with a sprinkling
of the inorganic salts known to be
essential for life. You seal the flask
and allow it to cool. After several
months, the liquid is as clear as
ever, and there are no signs of life.
A friend suggests that excluding
the air was a mistake, since most
life as we know it requires oxygen.
You repeat the experiment, but this
time you leave the flask open to the
atmosphere. To your great delight,
the liquid becomes cloudy after a
few days and under the microscope
you see beautiful small cells that
are clearly growing and dividing.
Does this experiment prove that
you managed to generate a novel
life-form? How might you redesign
your experiment to allow air
into the flask, yet eliminate the
possibility that contamination is
the explanation for the results?
(For a ready-made answer, look up
the classic experiments of Louis
Pasteur.)
To see the internal structure of a cell is difficult, not only because the
parts are small, but also because they are transparent and mostly colorless. One way around the problem is to stain cells with dyes that color
particular components differently (see Figure 1–5). Alternatively, one can
exploit the fact that cell components differ slightly from one another in
(A)
50 µm
(B)
50 µm
Figure 1–5 Cells form tissues in plants
and animals. (A) Cells in the root tip of a
fern. The nuclei are stained red, and each
cell is surrounded by a thin cell wall (light
blue). (B) Cells in the urine-collecting ducts
of the kidney. Each duct appears in this
cross section as a ring of closely packed
cells (with nuclei stained red ). The ring is
surrounded by extracellular matrix, stained
purple. (A, courtesy of James Mauseth;
B, from P.R. Wheater et al., Functional
Histology, 2nd ed. Edinburgh: Churchill
Livingstone, 1987. With permission from
Elsevier.)
7
8
Chapter 1
cytoplasm
Cells: The Fundamental Units of Life
plasma membrane
nucleus
(A)
Figure 1–6 Some of the internal
structures of a living cell can be seen
with a light microscope. (A) A cell taken
from human skin and grown in culture was
photographed through a light microscope
using interference-contrast optics (see Panel
1–1, pp. 10–11). The nucleus is especially
prominent. (B) A pigment cell from a frog,
stained with fluorescent dyes and viewed
with a confocal fluorescence microscope
(see Panel 1–1). The nucleus is shown in
purple, the pigment granules in red, and
the microtubules—a class of filaments built
from protein molecules in the cytoplasm—in
green. (A, courtesy of Casey Cunningham;
B, courtesy of Stephen Rogers and the
Imaging Technology Group of the Beckman
Institute, University of Illinois, Urbana.)
40 µm
(B)
10 µm
refractive index, just as glass differs in refractive index from water, causing light rays to be deflected as they pass from the one medium into the
other. The small differences in refractive index can be made visible by
specialized optical techniques, and the resulting images can be enhanced
further by electronic processing.
ECB4 e1.07/1.06
The cell thus revealed has a distinct anatomy (Figure 1–6A). It has
a sharply defined boundary, indicating the presence of an enclosing
membrane. A large, round structure, the nucleus, is prominent in the
middle of the cell. Around the nucleus and filling the cell’s interior is the
cytoplasm, a transparent substance crammed with what seems at first to
be a jumble of miscellaneous objects. With a good light microscope, one
can begin to distinguish and classify some of the specific components in
the cytoplasm, but structures smaller than about 0.2 μm—about half the
wavelength of visible light—cannot normally be resolved; points closer
than this are not distinguishable and appear as a single blur.
In recent years, however, new types of fluorescence microscopes have
been developed that use sophisticated methods of illumination and electronic image processing to see fluorescently labeled cell components in
much finer detail (Figure 1–6B). The most recent super-resolution fluorescence microscopes, for example, can push the limits of resolution
down even further, to about 20 nanometers (nm). That is the size of a
single ribosome, a large macromolecular complex composed of 80–90
individual proteins and RNA molecules.
The Fine Structure of a Cell Is Revealed by Electron
Microscopy
For the highest magnification and best resolution, one must turn to an
electron microscope, which can reveal details down to a few nanometers. Cell samples for the electron microscope require painstaking
preparation. Even for light microscopy, a tissue often has to be fixed (that
is, preserved by pickling in a reactive chemical solution), supported by
embedding in a solid wax or resin, cut or sectioned into thin slices, and
stained before it is viewed. For electron microscopy, similar procedures
are required, but the sections have to be much thinner and there is no
possibility of looking at living, wet cells.
Cells Under the Microscope
plasma membrane
nucleus
endoplasmic reticulum
ribosomes
mitochondrion
mitochondria
lysosome
peroxisome
(B)
(A)
2 µm
(C)
When thin sections are cut, stained, and placed in the electron microscope,
much of the jumble of cell components becomes sharply resolved into
distinct organelles—separate, recognizable substructures with speciale1.08/1.07
ized functions that are often only hazily defined withECB4
a light
microscope.
A delicate membrane, only about 5 nm thick, is visible enclosing the cell,
and similar membranes form the boundary of many of the organelles
inside (Figure 1–7A, B). The membrane that separates the interior of the
cell from its external environment is called the plasma membrane, while
the membranes surrounding organelles are called internal membranes.
All of these membranes are only two molecules thick (as discussed in
Chapter 11). With an electron microscope, even individual large molecules can be seen (Figure 1–7C).
The type of electron microscope used to look at thin sections of tissue is
known as a transmission electron microscope. This is, in principle, similar to a light microscope, except that it transmits a beam of electrons
rather than a beam of light through the sample. Another type of electron
microscope—the scanning electron microscope—scatters electrons off the
surface of the sample and so is used to look at the surface detail of cells
and other structures. A survey of the principal types of microscopy used
to examine cells is given in Panel 1–1 (pp. 10–11).
2 µm
50 nm
Figure 1–7 The fine structure of a cell
can be seen in a transmission electron
microscope. (A) Thin section of a liver cell
showing the enormous amount of detail that
is visible. Some of the components to be
discussed later in the chapter are labeled;
they are identifiable by their size and shape.
(B) A small region of the cytoplasm at higher
magnification. The smallest structures that
are clearly visible are the ribosomes, each
of which is made of 80–90 or so individual
large molecules. (C) Portion of a long,
threadlike DNA molecule isolated from a
cell and viewed by electron microscopy.
(A and B, courtesy of Daniel S. Friend;
C, courtesy of Mei Lie Wong.)
9
10
Panel 1–1
Microscopy
THE LIGHT MICROSCOPE
FLUORESCENCE
MICROSCOPY
retina
eye
eyepiece
2
eyepiece
beam-splitting
mirror
LIGHT
SOURCE
The light microscope allows us to
magnify cells up to 1000 times and to
resolve details as small as 0.2 µm
(a limitation imposed by the wavelike
nature of light, not by the quality of
the lenses). Three things are required
for viewing cells in a light microscope.
First, a bright light must be focused
onto the specimen by lenses in the
condenser. Second, the specimen must
be carefully prepared to allow light to
pass through it. Third, an appropriate
set of lenses (objective and eyepiece)
must be arranged to focus an image of
the specimen in the eye.
1
objective
object
specimen
Fluorescent dyes used for staining cells are detected with the
aid of a fluorescence microscope. This is similar to an
ordinary light microscope except that the illuminating light
is passed through two sets of filters. The first ( 1 ) filters the
light before it reaches the specimen, passing only those
wavelengths that excite the particular fluorescent dye. The
second ( 2 ) blocks out this light and passes only those
wavelengths emitted when the dye fluoresces. Dyed objects
show up in bright color on a dark background.
condenser
light
source
the light path in a
light microscope
LOOKING AT
LIVING CELLS
The same unstained, living
animal cell (fibroblast) in
culture viewed with
(A) straightforward
(bright-field) optics;
(B) phase-contrast optics;
(C) interference-contrast
optics. The two latter
systems exploit differences
in the way light travels
through regions of the cell
with differing refractive
indexes. All three images
can be obtained on the
same microscope simply by
interchanging optical
components.
(A)
(B)
(C)
FIXED SAMPLES
Most tissues are neither small enough nor
transparent enough to examine directly in
the microscope. Typically, therefore, they
are chemically fixed and cut into very thin
slices, or sections, that can be mounted on
a glass microscope slide and subsequently
stained to reveal different components of
the cells. A stained section of a plant root
tip is shown here (D). (Courtesy of
Catherine Kidner.)
objective lens
50 µm
(D)
50 µm
FLUORESCENT PROBES
Dividing nuclei in a fly embryo seen with a fluorescence
microscope after staining with specific fluorescent dyes.
Fluorescent dyes absorb light at one wavelength and
emit it at another, longer wavelength. Some such
dyes bind specifically to particular molecules in cells
and can reveal their location when examined with a
fluorescence microscope. An example is the stain for
DNA shown here (green ). Other dyes can be coupled
to antibody molecules, which then serve as highly
specific and versatile staining reagents that bind
selectively to particular large molecules, allowing us
to see their distribution in the cell. In the example
shown, a microtubule protein in the mitotic spindle
is stained red with a fluorescent antibody. (Courtesy
of William Sullivan.)
11
Cells Under the Microscope
CONFOCAL MICROSCOPY
A confocal microscope is a specialized type of fluorescence microscope that builds up an
image by scanning the specimen with a laser beam. The beam is focused onto a single
point at a specific depth in the specimen, and a pinhole aperture in the detector allows
only fluorescence emitted from this same point to be included in the image. Scanning the
beam across the specimen generates a sharp image of the plane of focus—an optical
section. A series of optical sections at different depths allows a three-dimensional image
to be constructed. An intact insect embryo is shown here stained with a fluorescent probe
for actin filaments. (A) Conventional fluorescence microscopy gives a blurry image due to
the presence of fluorescent structures above and below the plane of focus. (B) Confocal
microscopy provides an optical section showing the individual cells clearly. (Courtesy of
(A)
Richard Warn and Peter Shaw.)
(B)
SCANNING ELECTRON
MICROSCOPY
specimen
objective
lens
projector
lens
viewing
screen or
photographic
film
Courtesy of Philips Electron Optics, with
permission from FEI Co.
condenser
lens
Courtesy of Philips Electron Optics, with
permission from FEI Co.
TRANSMISSION
ELECTRON
MICROSCOPY
electron
gun
10 µm
electron
gun
condenser
lens
beam deflector
The electron micrograph below
shows a small region of a cell in
a piece of testis. The tissue has
been chemically fixed,
embedded in plastic, and cut
into very thin sections that have
then been stained with salts of
uranium and lead. (Courtesy of
Daniel S. Friend.)
scan
generator
video
screen
objective
lens
electrons from
specimen
detector
specimen
In the scanning electron microscope (SEM), the specimen, which
has been coated with a very thin film of a heavy metal, is scanned
by a beam of electrons brought to a focus on the specimen by
magnetic coils that act as lenses. The quantity of electrons
scattered or emitted as the beam bombards each successive point
on the surface of the specimen is measured by the detector, and is
used to control the intensity of successive points in an image built
up on a video screen. The microscope creates striking images of
three-dimensional objects with great depth of focus and can
resolve details down to somewhere between 3 nm and 20 nm,
depending on the instrument.
0.5 µm
The transmission electron microscope (TEM) is in principle similar
to a light microscope, but it uses a beam of electrons instead of a
beam of light, and magnetic coils to focus the beam instead of
glass lenses. The specimen, which is placed in a vacuum, must be
very thin. Contrast is usually introduced by staining the specimen
with electron-dense heavy metals that locally absorb or scatter
electrons, removing them from the beam as it passes through
the specimen. The TEM has a useful magnification of up to a
million-fold and can resolve details as small as about 1 nm in
biological specimens.
5 µm
Scanning electron micrograph
of stereocilia projecting from a
hair cell in the inner ear (left ).
For comparison, the same
structure is shown by light
microscopy, at the limit of its
resolution (above). (Courtesy of
Richard Jacobs and James
Hudspeth.)
1 µm
12
Chapter 1
0.2 mm
(200 µm)
Cells: The Fundamental Units of Life
minimum
resolvable by
unaided eye
CELLS
x10
20 µm
x10
20 mm
2 mm
0.2 mm
20 µm
2 µm
0.2 µm
20 nm
2 nm
0.2 nm
ORGANELLES
2 µm
x10
200 nm
minimum
resolvable
by light
microscope
x10
MOLECULES
20 nm
x10
2 nm
ATOMS
x10
minimum
resolvable
by electron
microscope
0.2 nm
1 m = 103 mm
= 106 µm
= 109 nm
(A)
(B)
Figure 1–8 How big is a cell and its components? (A) The sizes of cells and of their component parts, plus the
units in which they are measured. (B) Drawings to convey a sense of scale between living cells and atoms. Each
panel shows an image that is magnified by a factor of 10 compared to its predecessor—producing an imaginary
progression from a thumb, to skin, to skin cells, to a mitochondrion, to a ribosome, and ultimately to a cluster of
atoms forming part of one of the many ECB4
protein
molecules in our bodies. Note that ribosomes are present inside
e1.06,09/1.08
mitochondria (as shown here), as well as in the cytoplasm. Details of molecular structure, as shown in the last two
panels, are beyond the power of the electron microscope.
Even the most powerful electron microscopes, however, cannot visualize
the individual atoms that make up biological molecules (Figure 1–8). To
study the cell’s key components in atomic detail, biologists have developed
even more sophisticated tools. A technique called X-ray crystallography,
for example, is used to determine the precise three-dimensional structure
of protein molecules (discussed in Chapter 4).
The Prokaryotic Cell
Of all the types of cells revealed by the microscope, bacteria have the simplest structure and come closest to showing us life stripped down to its
essentials. Indeed, a bacterium contains essentially no organelles—not
even a nucleus to hold its DNA. This property—the presence or absence
of a nucleus—is used as the basis for a simple but fundamental classification of all living things. Organisms whose cells have a nucleus are called
eukaryotes (from the Greek words eu, meaning “well” or “truly,” and
karyon, a “kernel” or “nucleus”). Organisms whose cells do not have a
nucleus are called prokaryotes (from pro, meaning “before”). The terms
The Prokaryotic Cell
Figure 1–9 Bacteria come in different
shapes and sizes. Typical spherical, rodlike,
and spiral-shaped bacteria are drawn
to scale. The spiral cells shown are the
organisms that cause syphilis.
2 µm
spherical cells,
e.g., Streptococcus
rod-shaped cells,
e.g., Escherichia coli,
Salmonella
spiral cells,
e.g., Treponema pallidum
“bacterium” and “prokaryote” are often used interchangeably, although
we will see that the category of prokaryotes also includes another class
of cells, the archaea (singular archaeon), which are so remotely related to
ECB4
e1.10/1.09name.
bacteria that they are given
a separate
Prokaryotes are typically spherical, rodlike, or corkscrew-shaped (Figure
1–9). They are also small—generally just a few micrometers long,
although there are some giant species as much as 100 times longer than
this. Prokaryotes often have a tough protective coat, or cell wall, surrounding the plasma membrane, which encloses a single compartment
containing the cytoplasm and the DNA. In the electron microscope, the
cell interior typically appears as a matrix of varying texture, without any
obvious organized internal structure (Figure 1–10). The cells reproduce
quickly by dividing in two. Under optimum conditions, when food is plentiful, many prokaryotic cells can duplicate themselves in as little as 20
minutes. In 11 hours, by repeated divisions, a single prokaryote can give
rise to more than 8 billion progeny (which exceeds the total number of
humans presently on Earth). Thanks to their large numbers, rapid growth
rates, and ability to exchange bits of genetic material by a process akin
to sex, populations of prokaryotic cells can evolve fast, rapidly acquiring the ability to use a new food source or to resist being killed by a new
antibiotic.
Question 1–4
A bacterium weighs about 10–12 g
and can divide every 20 minutes.
If a single bacterial cell carried on
dividing at this rate, how long would
it take before the mass of bacteria
would equal that of the Earth
(6 × 1024 kg)? Contrast your result
with the fact that bacteria originated
at least 3.5 billion years ago and
have been dividing ever since.
Explain the apparent paradox. (The
number of cells N in a culture at
time t is described by the equation
N = N0 × 2t/G, where N0 is the
number of cells at zero time and G is
the population doubling time.)
Prokaryotes Are the Most Diverse and Numerous Cells
on Earth
Most prokaryotes live as single-celled organisms, although some join
together to form chains, clusters, or other organized multicellular structures. In shape and structure, prokaryotes may seem simple and limited,
but in terms of chemistry, they are the most diverse and inventive class of
cells. Members of this class exploit an enormous range of habitats, from
hot puddles of volcanic mud to the interiors of other living cells, and they
vastly outnumber all eukaryotic organisms on Earth. Some are aerobic,
using oxygen to oxidize food molecules; some are strictly anaerobic and
are killed by the slightest exposure to oxygen. As we discuss later in this
cytoplasm
cell wall
1 µm
Figure 1–10 The bacterium Escherichia
coli (E. coli ) has served as an important
model organism. An electron micrograph
of a longitudinal section is shown here;
the cell’s DNA is concentrated in the
lightly stained region. (Courtesy of
E. Kellenberger.)
13
14
Chapter 1
Cells: The Fundamental Units of Life
H
S
V
(A)
(B)
10 µm
1 µm
Figure 1–11 Some bacteria are photosynthetic. (A) Anabaena cylindrica forms
long, multicellular filaments. This light micrograph shows specialized cells that
either fix nitrogen (that is, capture N2 from the atmosphere and incorporate it into
ECB4
organic compounds; labeled H ), fix
COe1.12/1.11
2 through photosynthesis (labeled V ), or
become resistant spores (labeled S ). (B) An electron micrograph of a related species,
Phormidium laminosum, shows the intracellular membranes where photosynthesis
occurs. These micrographs illustrate that even some prokaryotes can form simple
multicellular organisms. (A, courtesy of David Adams; B, courtesy of D.P. Hill and
C.J. Howe.)
chapter, mitochondria—the organelles that generate energy in eukaryotic cells—are thought to have evolved from aerobic bacteria that took
to living inside the anaerobic ancestors of today’s eukaryotic cells. Thus
our own oxygen-based metabolism can be regarded as a product of the
activities of bacterial cells.
Virtually any organic, carbon-containing material—from wood to petroleum—can be used as food by one sort of bacterium or another. Even
more remarkably, some prokaryotes can live entirely on inorganic substances: they can get their carbon from CO2 in the atmosphere, their
nitrogen from atmospheric N2, and their oxygen, hydrogen, sulfur, and
phosphorus from air, water, and inorganic minerals. Some of these
prokaryotic cells, like plant cells, perform photosynthesis, using energy
from sunlight to produce organic molecules from CO2 (Figure 1–11); others derive energy from the chemical reactivity of inorganic substances in
the environment (Figure 1–12). In either case, such prokaryotes play a
unique and fundamental part in the economy of life on Earth: other living
things depend on the organic compounds that these cells generate from
inorganic materials.
Plants, too, can capture energy from sunlight and carbon from atmospheric CO2. But plants unaided by bacteria cannot capture N2 from the
atmosphere, and in a sense even plants depend on bacteria for photosynthesis. It is almost certain that the organelles in the plant cell that
6 µm
Figure 1–12 A sulfur bacterium gets its energy from H2S.
Beggiatoa, a prokaryote that lives in sulfurous environments, oxidizes
H2S to produce sulfur and can fix carbon even in the dark. In this light
micrograph, yellow deposits of sulfur can be seen inside both of the
cells. (Courtesy of Ralph W. Wolfe.)
The Eukaryotic Cell
perform photosynthesis—the chloroplasts—have evolved from photosynthetic bacteria that long ago found a home inside the cytoplasm of a plant
cell ancestor.
The World of Prokaryotes Is Divided into Two Domains:
Bacteria and Archaea
Traditionally, all prokaryotes have been classified together in one large
group. But molecular studies reveal that there is a gulf within the class
of prokaryotes, dividing it into two distinct domains called the bacteria
and the archaea. Remarkably, at a molecular level, the members of these
two domains differ as much from one another as either does from the
eukaryotes. Most of the prokaryotes familiar from everyday life—the species that live in the soil or make us ill—are bacteria. Archaea are found
not only in these habitats, but also in environments that are too hostile
for most other cells: concentrated brine, the hot acid of volcanic springs,
the airless depths of marine sediments, the sludge of sewage treatment
plants, pools beneath the frozen surface of Antarctica, and in the acidic,
oxygen-free environment of a cow’s stomach where they break down cellulose and generate methane gas. Many of these extreme environments
resemble the harsh conditions that must have existed on the primitive
Earth, where living things first evolved before the atmosphere became
rich in oxygen.
The Eukaryotic Cell
Eukaryotic cells, in general, are bigger and more elaborate than bacteria and archaea. Some live independent lives as single-celled organisms,
such as amoebae and yeasts (Figure 1–13); others live in multicellular
assemblies. All of the more complex multicellular organisms—including
plants, animals, and fungi—are formed from eukaryotic cells.
By definition, all eukaryotic cells have a nucleus. But possession of
a nucleus goes hand-in-hand with possession of a variety of other
organelles, most of which are membrane-enclosed and common to
all eukaryotic organisms. In this section, we take a look at the main
organelles found in eukaryotic cells from the point of view of their functions, and we consider how they came to serve the roles they have in the
life of the eukaryotic cell.
The Nucleus Is the Information Store of the Cell
The nucleus is usually the most prominent organelle in a eukaryotic cell
(Figure 1–14). It is enclosed within two concentric membranes that form
the nuclear envelope, and it contains molecules of DNA—extremely long
polymers that encode the genetic information of the organism. In the
light microscope, these giant DNA molecules become visible as individual
chromosomes when they become more compact before a cell divides
into two daughter cells (Figure 1–15). DNA also carries the genetic information in prokaryotic cells; these cells lack a distinct nucleus not because
they lack DNA, but because they do not keep their DNA inside a nuclear
envelope, segregated from the rest of the cell contents.
Figure 1–13 Yeasts are simple free-living eukaryotes. The
cells shown in this micrograph belong to the species of yeast,
Saccharomyces cerevisiae, used to make dough rise and turn
malted barley juice into beer. As can be seen in this image, the cells
reproduce by growing a bud and then dividing asymmetrically into a
large mother cell and a small daughter cell; for this reason, they are
called budding yeast.
10 µm
15
16
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–14 The nucleus contains most
of the DNA in a eukaryotic cell. (A) This
drawing of a typical animal cell shows its
extensive system of membrane-enclosed
organelles. The nucleus is colored brown,
the nuclear envelope is green, and the
cytoplasm (the interior of the cell outside
the nucleus) is white. (B) An electron
micrograph of the nucleus in a mammalian
cell. Individual chromosomes are not visible
because at this stage of the cell’s growth
its DNA molecules are dispersed as fine
threads throughout the nucleus. (B, courtesy
of Daniel S. Friend.)
nuclear
envelope
nucleus
(A)
(B)
2 µm
Mitochondria Generate Usable Energy from Food to
Power the Cell
Mitochondria are present in essentially all eukaryotic cells, and they are
among the most conspicuous organelles in the cytoplasm (see Figure
1–7B). In a fluorescence microscope, they appear as worm-shaped structures that often form branching networks (Figure 1–16). When seen
with an electron microscope, individual mitochondria are found to be
enclosed in two separate membranes, with the inner membrane formed
into folds that project into the interior of the organelle (Figure 1–17).
Microscopic examination by itself, however, gives little indication ­of
what mitochondria do. Their function was discovered by breaking open
cells and then spinning the soup of cell fragments in a centrifuge; this
nucleus
Figure 1–15 Chromosomes become
visible when a cell is about to divide.
As a eukaryotic cell prepares to divide, its
DNA molecules become progressively more
compacted (condensed), forming wormlike
chromosomes that can be distinguished
in the light microscope. The photographs
show three successive steps in this process
in a cultured cell from a newt’s lung; note
that in the last micrograph on the right,
the nuclear envelope has broken down.
(Courtesy of Conly L. Rieder.)
ECB4 e1.15/1.14
nuclear envelope
condensed chromosomes
25 µm
The Eukaryotic Cell
Figure 1–16 Mitochondria can be variable in shape and size. This
budding yeast cell, which contains a green fluorescent protein in its
mitochondria, was viewed in a super-resolution confocal fluorescence
microscope. In this three-dimensional image, the mitochondria are
seen to form complex branched networks. (From A. Egner et al., Proc.
Natl Acad. Sci. USA 99:3370–3375, 2002. With permission from the
National Academy of Sciences.)
separates the organelles according to their size and density. Purified
mitochondria were then tested to see what chemical processes they
could perform. This revealed that mitochondria are generators of chemical energy for the cell. They harness the energy from the oxidation of food
molecules, such as sugars, to produce adenosine triphosphate, or ATP—
the basic chemical fuel that powers most of the cell’s activities. Because
the mitochondrion consumes oxygen and releases carbon dioxide in the
course of this activity, the entire process is called cellular respiration—
essentially, breathing on a cellular level. Without mitochondria, animals,
fungi, and plants would be unable to use oxygen to extract the energy
they need from the food molecules that nourish them. The process of cellular respiration is considered in detail in Chapter 14.
outer membrane
10 µm
ECB4 n1.102/1.16
inner membrane
(B)
(C)
(A)
100 nm
Figure 1–17 Mitochondria have a distinctive structure. (A) An electron micrograph of a cross section of a mitochondrion reveals
the extensive infolding of the inner membrane. (B) This three-dimensional representation of the arrangement of the mitochondrial
membranes shows the smooth outer membrane (gray) and the highly convoluted inner membrane (red ). The inner membrane contains
most of the proteins responsible for cellular respiration—one of the mitochondrion’s main functions—and it is highly folded to provide
a large surface area for this activity. (C) In this schematic cell, the interior space of the mitochondrion is colored orange. (A, courtesy of
Daniel S. Friend.)
ECB4 e1.18/1.17
17
18
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–18 Mitochondria most likely
evolved from engulfed bacteria. It is
virtually certain that mitochondria originate
from bacteria that were engulfed by an
ancestral pre-eukaryotic cell and survived
inside it, living in symbiosis with their host.
Note that the double membrane of presentday mitochondria is thought to have been
derived from the plasma membrane and
outer membrane of the engulfed bacterium.
anaerobic
pre-eukaryotic cell
early aerobic
eukaryotic cell
internal
membranes
nucleus
bacterial outer membrane
loss of membrane
derived from
pre-eukaryotic cell
bacterial plasma
membrane
mitochondria with
double membrane
aerobic bacterium
Mitochondria contain their own DNA and reproduce by dividing in two.
Because they resemble bacteria in so many ways, they are thought to
have been derived from bacteria that were engulfed by some ancestor
of present-day eukaryotic cells (Figure 1–18). This evidently created a
symbiotic relationship in which the host eukaryote and the engulfed bacterium helped one another to survive and reproduce.
Chloroplasts Capture Energy from Sunlight
Chloroplasts are large, green organelles that are found only in the cells
of plants and algae, not in the cells of animals or fungi. These organelles
have an even more complex structure than mitochondria: in addition to
their two surrounding membranes, they possess internal stacks of membranes containing the green pigment chlorophyll (Figure 1–19).
Chloroplasts carry out photosynthesis—trapping the energy of sunlight in their chlorophyll molecules and using this energy to drive the
MBoC6
manufacture of energy-rich
sugarm12.04/12.04
molecules. In the process, they release
chloroplasts
chlorophyllcontaining
membranes
Figure 1–19 Chloroplasts in plant cells
capture the energy of sunlight.
(A) A single cell isolated from a leaf
of a flowering plant, seen in the light
microscope, showing many green
chloroplasts. (B) A drawing of one of the
chloroplasts, showing the inner and outer
membranes, as well as the highly folded
system of internal membranes containing
the green chlorophyll molecules that absorb
light energy. (A, courtesy of Preeti Dahiya.)
inner
membrane
outer
membrane
(A)
10 µm
(B)
The Eukaryotic Cell
early
eukaryotic cell
eukaryotic cell
capable of
photosynthesis
chloroplasts
photosynthetic
bacterium
oxygen as a molecular by-product. Plant cells can then extract this stored
chemical energy when they need it, by oxidizing these sugars in their
mitochondria, just as animalECB4
cells e1.21/1.20
do. Chloroplasts thus enable plants to
get their energy directly from sunlight. And they allow plants to produce
the food molecules—and the oxygen—that mitochondria use to generate
chemical energy in the form of ATP. How these organelles work together
is discussed in Chapter 14.
Like mitochondria, chloroplasts contain their own DNA, reproduce
by dividing in two, and are thought to have evolved from bacteria—in
this case, from photosynthetic bacteria that were engulfed by an early
eukaryotic cell (Figure 1–20).
Internal Membranes Create Intracellular Compartments
with Different Functions
Nuclei, mitochondria, and chloroplasts are not the only membraneenclosed organelles inside eukaryotic cells. The cytoplasm contains a
profusion of other organelles that are surrounded by single membranes
(see Figure 1–7A). Most of these structures are involved with the cell’s
ability to import raw materials and to export both the useful substances
and waste products that are produced by the cell.
The endoplasmic reticulum (ER) is an irregular maze of interconnected
spaces enclosed by a membrane (Figure 1–21). It is the site where most
cell-membrane components, as well as materials destined for export
from the cell, are made. This organelle is enormously enlarged in cells
that are specialized for the secretion of proteins. Stacks of flattened,
membrane-enclosed sacs constitute the Golgi apparatus (Figure 1–22),
which modifies and packages molecules made in the ER that are destined
to be either secreted from the cell or transported to another cell compartment. Lysosomes are small, irregularly shaped organelles in which
intracellular digestion occurs, releasing nutrients from ingested food particles and breaking down unwanted molecules for either recycling within
the cell or excretion from the cell. Indeed, many of the large and small
molecules within the cell are constantly being broken down and remade.
Peroxisomes are small, membrane-enclosed vesicles that provide a safe
environment for a variety of reactions in which hydrogen peroxide is
used to inactivate toxic molecules. Membranes also form many different
types of small transport vesicles that ferry materials between one membrane-enclosed organelle and another. All of these membrane-enclosed
organelles are sketched in Figure 1–23A.
Figure 1–20 Chloroplasts almost certainly
evolved from engulfed photosynthetic
bacteria. The bacteria are thought to have
been taken up by early eukaryotic cells that
already contained mitochondria.
19
20
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–21 The endoplasmic reticulum
produces many of the components
of a eukaryotic cell. (A) Schematic
diagram of an animal cell shows the
endoplasmic reticulum (ER) in green.
(B) Electron micrograph of a thin section
of a mammalian pancreatic cell shows a
small part of the ER, of which there are
vast amounts in this cell type, which is
specialized for protein secretion. Note that
the ER is continuous with the membranes
of the nuclear envelope. The black particles
studding the particular region of the ER
shown here are ribosomes, structures that
translate RNAs into proteins. Because of its
appearance, ribosome-coated ER is often
called “rough ER” to distinguish it from
the “smooth ER,” which does not have
ribosomes bound to it. (B, courtesy of
Lelio Orci.)
nucleus
nuclear envelope
endoplasmic reticulum
(A)
(B)
ribosomes
1 µm
A continual exchange of materials takes place between the endoplasmic
reticulum, the Golgi apparatus, the lysosomes, and the outside of the cell.
The exchange is mediated by transport vesicles that pinch off from the
membrane of one organelle and fuse with another, like tiny soap bubbles
budding from and rejoining larger bubbles. At the surface of the cell, for
example, portions of the plasma membrane tuck inward and pinch off
to form vesicles that carry material captured from the external medium
ECB4 endocytosis
e1.22/1.21 (Figure 1–24). Animal cells can
into the cell—a process called
nuclear
envelope
(A)
Figure 1–22 The Golgi apparatus is
composed of a stack of flattened discs.
(A) Schematic diagram of an animal cell with
the Golgi apparatus colored red. (B) More
realistic drawing of the Golgi apparatus.
Some of the vesicles seen nearby have
pinched off from the Golgi stack; others are
destined to fuse with it. Only one stack is
shown here, but several can be present in a
cell. (C) Electron micrograph that shows the
Golgi apparatus from a typical animal cell.
(C, courtesy of Brij J. Gupta.)
(B)
membraneenclosed vesicles
Golgi apparatus
endoplasmic reticulum
(C)
1 µm
The Eukaryotic Cell
mitochondrion
lysosome
peroxisome
cytosol
nuclear
envelope
vesicle
(A)
Golgi
apparatus
endoplasmic
reticulum
(B)
Figure 1–23 Membrane-enclosed
organelles are distributed throughout
the eukaryotic cell cytoplasm. (A) The
membrane-enclosed organelles, shown
in different colors, are each specialized
to perform a different function. (B) The
cytoplasm that fills the space outside
of these organelles is called the cytosol
(colored blue).
plasma
membrane
engulf very large particles, or even entire foreign cells, by endocytosis. In
the reverse process, called exocytosis, vesicles from inside the cell fuse
ECB4
e1.24/1.23
with the plasma membrane
and
release their contents into the external
medium (see Figure 1–24); most of the hormones and signal molecules
that allow cells to communicate with one another are secreted from cells
by exocytosis. How membrane-enclosed organelles move proteins and
other molecules from place to place inside the cell is discussed in detail
in Chapter 15.
The Cytosol Is a Concentrated Aqueous Gel of Large and
Small Molecules
If we were to strip the plasma membrane from a eukaryotic cell and then
remove all of its membrane-enclosed organelles, including the nucleus,
endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplasts, and
so on, we would be left with the cytosol (see Figure 1–23B). In other
words, the cytosol is the part of the cytoplasm that is not contained within
intracellular membranes. In most cells, the cytosol is the largest single
compartment. It contains a host of large and small molecules, crowded
together so closely that it behaves more like a water-based gel than a
liquid solution (Figure 1–25). The cytosol is the site of many chemical
reactions that are fundamental to the cell’s existence. The early steps in
the breakdown of nutrient molecules take place in the cytosol, for example, and it is here that most proteins are made by ribosomes.
IMPORT BY ENDOCYTOSIS
The Cytoskeleton Is Responsible for Directed Cell
Movements
The cytoplasm is not just a structureless soup of chemicals and organelles.
Using an electron microscope, one can see that in eukaryotic cells the
cytosol is criss-crossed by long, fine filaments. Frequently, the filaments
are seen to be anchored at one end to the plasma membrane or to radiate out from a central site adjacent to the nucleus. This system of protein
filaments, called the cytoskeleton, is composed of three major filament
types (Figure 1–26). The thinnest of these filaments are the actin filaments; they are abundant in all eukaryotic cells but occur in especially
large numbers inside muscle cells, where they serve as a central part
of the machinery responsible for muscle contraction. The thickest filaments in the cytosol are called microtubules, because they have the form
of minute hollow tubes. In dividing cells, they become reorganized into a
spectacular array that helps pull the duplicated chromosomes in opposite
plasma
membrane
EXPORT BY EXOCYTOSIS
Figure 1–24 Eukaryotic cells engage in
continual endocytosis and exocytosis.
They import extracellular materials by
endocytosis and secrete intracellular
ECB4 by
e1.25/1.24
materials
exocytosis.
21
22
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–25 The cytoplasm is stuffed with
organelles and a host of large and small
molecules. This schematic drawing, which
extends across two pages and is based
on the known sizes and concentrations
of molecules in the cytosol, shows how
crowded the cytoplasm is. Proteins are blue,
membrane lipids are yellow, and ribosomes
and DNA are pink. The panorama begins on
the far left at the plasma membrane, moves
through the endoplasmic reticulum, Golgi
apparatus, and a mitochondrion, and ends
on the far right in the nucleus. (Courtesy of
D. Goodsell.)
Question 1–5
Suggest a reason why it would be
advantageous for eukaryotic cells to
evolve elaborate internal membrane
systems that allow them to import
substances from the outside, as
shown in Figure 1–24.
Figure 1–26 The cytoskeleton is a
network of protein filaments that crisscrosses the cytoplasm of eukaryotic
cells. The three major types of filaments
can be detected using different fluorescent
stains. Shown here are (A) actin filaments,
(B) microtubules, and (C) intermediate
filaments. (A, courtesy of Simon Barry
and Chris D’Lacey; B, courtesy of Nancy
Kedersha; C, courtesy of Clive Lloyd.)
directions and distribute them equally to the two daughter cells (Figure
1–27). Intermediate in thickness between actin filaments and microtubules are the intermediate filaments, which serve to strengthen the cell.
These three types of filaments, together with other proteins that attach to
them, form
system of girders, ropes, and motors that gives the cell its
ECB4 ae1.26/1.25a
mechanical strength, controls its shape, and drives and guides its movements (Movie 1.2 and Movie 1.3).
Because the cytoskeleton governs the internal organization of the cell
as well as its external features, it is as necessary to a plant cell—boxed
in by a tough wall of extracellular matrix—as it is to an animal cell that
freely bends, stretches, swims, or crawls. In a plant cell, for example,
organelles such as mitochondria are driven in a constant stream around
the cell interior along cytoskeletal tracks (Movie 1.4). And animal cells
and plant cells alike depend on the cytoskeleton to separate their internal
components into two daughter cells during cell division (see Figure 1–27).
The cytoskeleton’s role in cell division may be its most ancient function. Even bacteria contain proteins that are distantly related to those of
eukaryotic actin filaments and microtubules, forming filaments that play
a part in prokaryotic cell division. We examine the cytoskeleton in detail
in Chapter 17, discuss its role in cell division in Chapter 18, and review
how it responds to signals from outside the cell in Chapter 16.
The Cytoplasm Is Far from Static
The cell interior is in constant motion. The cytoskeleton is a dynamic
jungle of protein ropes that are continually being strung together and
taken apart; its filaments can assemble and then disappear in a matter
of minutes. Motor proteins use the energy stored in molecules of ATP to
trundle along these tracks and cables, carrying organelles and proteins
throughout the cytoplasm, and racing across the width of the cell in seconds. In addition, the large and small molecules that fill every free space
in the cell are swept to and fro by random thermal motion, constantly
colliding with one another and with other structures in the cell’s crowded
cytoplasm (Movie 1–5).
(A)
50 µm
(B)
(C)
The Eukaryotic Cell
Of course, neither the bustling nature of the cell’s interior nor the details
of cell structure were appreciated when scientists first peered at cells in
a microscope; our knowledge of cell structure accumulated slowly. A few
of the key discoveries are listed in Table 1–1. In addition, Panel 1–2 summarizes the differences between animal, plant, and
bacterial
cells.
ECB4
e1.26/1.25b
Eukaryotic Cells May Have Originated as Predators
Eukaryotic cells are typically 10 times the length and 1000 times the volume of prokaryotic cells, although there is huge size variation within
each category. They also possess a whole collection of features—a
cytoskeleton, mitochondria, and other organelles—that set them apart
from bacteria and archaea.
When and how eukaryotes evolved these systems remains something of a
mystery. Although eukaryotes, bacteria, and archaea must have diverged
from one another very early in the history of life on Earth (discussed in
Chapter 14), the eukaryotes did not acquire all of their distinctive features
at the same time (Figure 1–28). According to one theory, the ancestral
eukaryotic cell was a predator that fed by capturing other cells. Such a
way of life requires a large size, a flexible membrane, and a cytoskeleton to help the cell move and eat. The nuclear compartment may have
evolved to keep the DNA segregated from this physical and chemical
hurly-burly, so as to allow more delicate and complex control of the way
the cell reads out its genetic information.
Such a primitive cell, witha nucleus and cytoskeleton, was most likely
the sort of cell that engulfed the free-living, oxygen-consuming bacteria that were the likely ancestors of the mitochondria (see Figure 1–18).
This partnership is thought to have been established 1.5 billion years ago,
when the Earth’s atmosphere first became rich in oxygen. A subset of
Question 1–6
Discuss the relative advantages
and disadvantages of light and
electron microscopy. How could
you best visualize (a) a living skin
cell, (b) a yeast mitochondrion, (c) a
bacterium, and (d) a microtubule?
duplicated
chromosomes
microtubules
Figure 1–27 Microtubules help distribute
the chromosomes in a dividing cell.
When a cell divides, its nuclear envelope
breaks down and its DNA condenses into
visible chromosomes, each of which has
duplicated to form a pair of conjoined
chromosomes that will ultimately be pulled
apart into separate cells by microtubules. In
the transmission electron micrograph (left),
the microtubules are seen to radiate from
foci at opposite ends of the dividing cell.
(Photomicrograph courtesy of
Conly L. Rieder.)
23
24
Chapter 1
Cells: The Fundamental Units of Life
Table 1–1 Historical Landmarks in Determining Cell Structure
1665
Hooke uses a primitive microscope to describe small chambers in sections of cork that he calls “cells.”
1674
Leeuwenhoek reports his discovery of protozoa. Nine years later, he sees bacteria for the first time.
1833
Brown publishes his microscopic observations of orchids, clearly describing the cell nucleus.
1839
Schleiden and Schwann propose the cell theory, stating that the nucleated cell is the universal building block of plant
and animal tissues.
1857
Kölliker describes mitochondria in muscle cells.
1879
Flemming describes with great clarity chromosome behavior during mitosis in animal cells.
1881
Cajal and other histologists develop staining methods that reveal the structure of nerve cells and the organization of
neural tissue.
1898
Golgi first sees and describes the Golgi apparatus by staining cells with silver nitrate.
1902
Boveri links chromosomes and heredity by observing chromosome behavior during sexual reproduction.
1952
Palade, Porter, and Sjöstrand develop methods of electron microscopy that enable many intracellular structures to be
seen for the first time. In one of the first applications of these techniques, Huxley shows that muscle contains arrays of
protein filaments—the first evidence of a cytoskeleton.
1957
Robertson describes the bilayer structure of the cell membrane, seen for the first time in the electron microscope.
1960
Kendrew describes the first detailed protein structure (sperm whale myoglobin) to a resolution of 0.2 nm using X-ray
crystallography. Perutz proposes a lower-resolution structure for hemoglobin.
1965
Christian de Duve and his colleagues use a cell-fractionation technique to separate peroxisomes, mitochondria, and
lysosomes from a preparation of rat liver.
1968
Petran and collaborators make the first confocal microscope.
1970
Frye and Edidin use fluorescent antibodies to show that plasma membrane molecules can diffuse in the plane of the
membrane, indicating that cell membranes are fluid.
1974
Lazarides and Weber use fluorescent antibodies to stain the cytoskeleton.
1994
Chalfie and collaborators introduce green fluorescent protein (GFP) as a marker to follow the behavior of proteins in
living cells.
these cells later acquired chloroplasts by engulfing photosynthetic bacteria (see Figure 1–20). The likely history of these endosymbiotic events is
illustrated in Figure 1–28.
That single-celled eukaryotes can prey upon and swallow other cells
is borne out by the behavior of many of the free-living, actively motile
nonphotosynthetic
bacteria
photosynthetic
bacteria
plants
animals
fungi
chloroplasts
mitochondria
TIME
Figure 1–28 Where did eukaryotes
come from? The eukaryotic, bacterial,
and archaean lineages diverged from one
another very early in the evolution of life
on Earth. Some time later, eukaryotes are
thought to have acquired mitochondria;
later still, a subset of eukaryotes acquired
chloroplasts. Mitochondria are essentially
the same in plants, animals, and fungi, and
therefore were presumably acquired before
these lines diverged.
bacteria
anaerobic ancestral eukaryote
ancestral prokaryote
archaea
archaea
Panel 1–2
CELL ARCHITECTURE
ANIMAL CELL
25
microtubule
centrosome with a
pair of centrioles
extracellular matrix
chromatin (DNA)
nuclear pore
nuclear envelope
vesicles
lysosome
actin
filaments
5 µm
nucleolus
peroxisome
ribosome
Golgi apparatus
intermediate
filaments
plasma membrane
nucleus
Golgi
apparatus
flagellum
ribosomes in
cytosol
Three cell types are drawn
here in a more realistic
manner than in the schematic
drawing in Figure 1–23. The
same colors are used, however,
to distinguish the organelles
of the cell. The animal cell
drawing is based on a
fibroblast, a cell that
inhabits connective tissue
and deposits extracellular
matrix. A micrograph of a
living fibroblast is shown in
Figure 1–6A. The plant cell
drawing is typical of a young
leaf cell. The bacterium shown
is rod-shaped and has a single
flagellum for motility; note its
much smaller size (compare
scale bars).
endoplasmic
reticulum
mitochondrion
nucleolus
chromatin
(DNA)
nuclear
pore
cell wall
microtubule
vacuole
(fluid-filled)
peroxisome
DNA
chloroplast
plasma membrane
cell wall
ribosomes
in cytosol
actin filaments
BACTERIAL CELL
1 µm
PLANT CELL
vacuole membrane (tonoplast)
lysosome
5 µm
26
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–29 One protozoan eats another.
(A) The scanning electron micrograph shows
Didinium on its own, with its circumferential
rings of beating cilia and its “snout” at the
top. (B) Didinium is seen ingesting another
ciliated protozoan, a Paramecium. (Courtesy
of D. Barlow.)
(A)
100 µm
(B)
microorganisms called protozoans. Didinium, for example, is a large,
carnivorous protozoan with a diameter of about 150 μm—roughly 10
times that of the average human cell. It has a globular body encircled by
ECB4 end
e1.30/1.29
two fringes of cilia, and its front
is flattened except for a single protrusion rather like a snout (Figure 1–29A). Didinium swims at high speed
by means of its beating cilia. When it encounters a suitable prey, usually
another type of protozoan, it releases numerous small, paralyzing darts
from its snout region. Didinium then attaches to and devours the other
cell, inverting like a hollow ball to engulf its victim, which can be almost
as large as itself (Figure 1–29B).
Not all protozoans are predators. They can be photosynthetic or carnivorous, motile or sedentary. Their anatomy is often elaborate and includes
such structures as sensory bristles, photoreceptors, beating cilia, stalklike appendages, mouthparts, stinging darts, and musclelike contractile
bundles (Figure 1–30). Although they are single cells, protozoans can be
as intricate and versatile as many multicellular organisms. Much remains
to be learned about fundamental cell biology from studies of these fascinating life-forms.
Model Organisms
All cells are thought to be descended from a common ancestor, whose
fundamental properties have been conserved through evolution. Thus
knowledge gained from the study of one organism contributes to our
understanding of others, including ourselves. But certain organisms are
easier than others to study in the laboratory. Some reproduce rapidly and
are convenient for genetic manipulations; others are multicellular but
transparent, so that one can directly watch the development of all their
internal tissues and organs. For reasons such as these, large communities of biologists have become dedicated to studying different aspects of
the biology of a few chosen species, pooling their knowledge to gain a
deeper understanding than could be achieved if their efforts were spread
over many different species. Although the roster of these representative organisms is continually expanding, a few stand out in terms of the
breadth and depth of information that has been accumulated about them
over the years—knowledge that contributes to our understanding of how
all cells work. In this section, we examine some of these model organisms and review the benefits that each offers to the study of cell biology
and, in many cases, to the promotion of human health.
Model Organisms
(C)
(A)
(B)
(D)
(E)
(F)
(G)
Figure 1–30 An assortment of protozoans illustrates the enormous variety within this class of single-celled
microorganisms. These drawings are done to different scales, but in each case the scale bar represents
10 μm. The organisms in (A), (C), and (G) are ciliates; (B) is a heliozoan; (D) is an amoeba; (E) is a dinoflagellate; and
(F) is a euglenoid. To see the latter in action, watch Movie 1.6. (From M.A. Sleigh, The Biology of Protozoa. London:
Edward Arnold, 1973. With permission from Edward Arnold.)
Molecular Biologists Have Focused on E. coli
In molecular terms, we understand the workings of the bacterium
Escherichia coli—E. coli for short—more thoroughly
than those of any
ECB4 e1.31/1.30
other living organism (see Figure 1–10). This small, rod-shaped cell normally lives in the gut of humans and other vertebrates, but it also grows
happily and reproduces rapidly in a simple nutrient broth in a culture
bottle.
Most of our knowledge of the fundamental mechanisms of life—including
how cells replicate their DNA and how they decode these genetic instructions to make proteins—has come from studies of E. coli. Subsequent
research has confirmed that these basic processes occur in essentially the
same way in our own cells as they do in E. coli.
Brewer’s Yeast Is a Simple Eukaryotic Cell
We tend to be preoccupied with eukaryotes because we are eukaryotes ourselves. But human cells are complicated and reproduce relatively
slowly. To get a handle on the fundamental biology of eukaryotic cells,
it is often advantageous to study a simpler cell that reproduces more
rapidly. A popular choice has been the budding yeast Saccharomyces
cerevisiae (Figure 1–31)—the same microorganism that is used for brewing beer and baking bread.
S. cerevisiae is a small, single-celled fungus that is at least as closely
related to animals as it is to plants. Like other fungi, it has a rigid cell wall,
is relatively immobile, and possesses mitochondria but not chloroplasts.
When nutrients are plentiful, S. cerevisiae reproduces almost as rapidly as
a bacterium. Yet it carries out all the basic tasks that every eukaryotic cell
must perform. Genetic and biochemical studies in yeast have been crucial
to understanding many basic mechanisms in eukaryotic cells, including
the cell-division cycle—the chain of events by which the nucleus and all
the other components of a cell are duplicated and parceled out to create
two daughter cells. The machinery that governs cell division has been
Question 1–7
Your next-door neighbor has
donated $100 in support of cancer
research and is horrified to learn
that her money is being spent on
studying brewer’s yeast. How could
you put her mind at ease?
27
28
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–31 The yeast Saccharomyces cerevisiae is a model
eukaryote. In this scanning electron micrograph, a few yeast cells are
seen in the process of dividing, which they do by budding. Another
micrograph of the same species is shown in Figure 1–13. (Courtesy of
Ira Herskowitz and Eric Schabatach.)
so well conserved over the course of evolution that many of its components can function interchangeably in yeast and human cells (see How
We Know, pp. 30–31). Darwin himself would no doubt have been stunned
by this dramatic example of evolutionary conservation.
Arabidopsis Has Been Chosen as a Model Plant
10 µm
The large multicellular organisms that we see around us—both plants
and animals—seem fantastically varied, but they are much closer to one
another in their evolutionary origins, and more similar in their basic
cell biology, than the great host of microscopic single-celled organisms.
Whereas bacteria, archaea, and eukaryotes separated from each other
more than 3 billion years ago, plants, animals, and fungi diverged only
about 1.5 billion years ago, and the different species of flowering plants
less than 200 million years ago.
The close evolutionary relationship among all flowering plants means
that we can gain insight into their cell and molecular biology by focusing
on just a few convenient species for detailed analysis. Out of the several
hundred thousand species of flowering plants on Earth today, molecular
biologists have focused their efforts on a small weed, the common wall
cress Arabidopsis thaliana (Figure 1–32), which can be grown indoors
in large numbers: one plant can produce thousands of offspring within
8–10 weeks. Because genes found in Arabidopsis have counterparts in
agricultural species, studying this simple weed provides insights into
the development and physiology of the crop plants upon which our lives
depend, as well as into the evolution of all the other plant species that
dominate nearly every ecosystem on Earth.
ECB4 e1.32/1.31
Model Animals Include Flies, Fish, Worms, and Mice
Multicellular animals account for the majority of all named species of
living organisms, and the majority of animal species are insects. It is fitting, therefore, that an insect, the small fruit fly Drosophila melanogaster
(Figure 1–33), should occupy a central place in biological research. In
fact, the foundations of classical genetics were built to a large extent on
studies of this insect. More than 80 years ago, genetic analysis of the fruit
fly provided definitive proof that genes—the units of heredity—are carried on chromosomes. In more recent times, Drosophila, more than any
other organism, has shown us how the genetic instructions encoded in
DNA molecules direct the development of a fertilized egg cell (or zygote)
into an adult multicellular organism containing vast numbers of different
cell types organized in a precise and predictable way. Drosophila mutants
with body parts strangely misplaced or oddly patterned have provided
the key to identifying and characterizing the genes that are needed to
make a properly structured adult body, with gut, wings, legs, eyes, and
all the other bits and pieces in their correct places. These genes—which
are copied and passed on to every cell in the body—define how each cell
will behave in its social interactions with its sisters and cousins, thus
controlling the structures that the cells can create. Moreover, the genes
1 cm
Figure 1–32 Arabidopsis thaliana, the common wall cress, is a
model plant. This small weed has become the favorite organism
of plant molecular and developmental biologists. (Courtesy of Toni
Hayden and the John Innes Centre.)
Model Organisms
Figure 1–33 Drosophila melanogaster is a
favorite among developmental biologists
and geneticists. Molecular genetic studies
on this small fly have provided a key to the
understanding of how all animals develop.
(Courtesy of E.B. Lewis.)
1 mm
responsible for the development of Drosophila have turned out to be
amazingly similar to those of humans—far more similar than one would
suspect from outward appearances. Thus the fly serves as a valuable
model for studying human development and disease.
Another widely studied organism is the nematode worm Caenorhabditis
elegans (Figure 1–34), a harmless
relative of the eelworms that attack the
ECB4 e1.34/1.33
roots of crops. Smaller and simpler than Drosophila, this creature develops with clockwork precision from a fertilized egg cell into an adult that
has exactly 959 body cells (plus a variable number of egg and sperm
cells)—an unusual degree of regularity for an animal. We now have a
minutely detailed description of the sequence of events by which this
occurs—as the cells divide, move, and become specialized according to
strict and predictable rules. And a wealth of mutants are available for
testing how the worm’s genes direct this developmental ballet. Some 70%
of human genes have some counterpart in the worm, and C. elegans, like
Drosophila, has proved to be a valuable model for many of the developmental processes that occur in our own bodies. Studies of nematode
development, for example, have led to a detailed molecular understanding of apoptosis, a form of programmed cell death by which surplus cells
are disposed of in all animals—a topic of great importance for cancer
research (discussed in Chapters 18 and 20).
Another organism that is providing molecular insights into developmental processes, particularly in vertebrates, is the zebrafish. Because this
0.2 mm
Figure 1–34 Caenorhabditis elegans is a small nematode worm that normally
lives in the soil. Most individuals are hermaphrodites, producing both sperm and
eggs (the latter of which can be seen along the underside of the animal). C. elegans
was the first multicellular organism to have its complete genome sequenced.
(Courtesy of Maria Gallegos.)
29
30
How we Know
life’s common mechanisms
All living things are made of cells, and all cells—as we
have discussed in this chapter—are fundamentally similar inside: they store their genetic instructions in DNA
molecules, which direct the production of RNA molecules, which in turn direct the production of proteins.
It is largely the proteins that carry out the cell’s chemical reactions, give the cell its shape, and control its
behavior. But how deep do these similarities between
cells—and the organisms they comprise—really run?
Are parts from one organism interchangeable with parts
from another? Would an enzyme that breaks down glucose in a bacterium be able to digest the same sugar if it
were placed inside a yeast cell or a cell from a lobster or
a human? What about the molecular machines that copy
and interpret genetic information? Are they functionally
equivalent from one organism to another? Insights have
come from many sources, but the most stunning and
dramatic answer came from experiments performed on
humble yeast cells. These studies, which shocked the
biological community, focused on one of the most fundamental processes of life—cell division.
Division and discovery
All cells come from other cells, and the only way to
make a new cell is through division of a preexisting
one. To reproduce, a parent cell must execute an orderly
sequence of reactions, through which it duplicates its
contents and divides in two. This critical process of
duplication and division—known as the cell-division
cycle, or cell cycle for short—is complex and carefully
controlled. Defects in any of the proteins involved can
be devastating to the cell.
Fortunately for biologists, this acute reliance on crucial proteins makes them easy to identify and study. If a
protein is essential for a given process, a mutation that
results in an abnormal protein—or in no protein at all—
can prevent the cell from carrying out the process. By
isolating organisms that are defective in their cell-division cycle, scientists have worked backward to discover
the proteins that control progress through the cycle.
The study of cell-cycle mutants has been particularly
successful in yeasts. Yeasts are unicellular fungi and are
popular organisms for such genetic studies. They are
eukaryotes, like us, but they are small, simple, rapidly
reproducing, and easy to manipulate genetically. Yeast
mutants that are defective in their ability to complete
cell division have led to the discovery of many genes
that control the cell-division cycle—the so-called Cdc
genes—and have provided a detailed understanding of
how these genes, and the proteins they encode, actually
work.
Paul Nurse and his colleagues used this approach to
identify Cdc genes in the yeast Schizosaccharomyces
pombe, which is named after the African beer from
which it was first isolated. S. pombe is a rod-shaped cell,
which grows by elongation at its ends and divides by fission into two, through the formation of a partition in the
center of the rod. The researchers found that one of the
Cdc genes they had identified, called Cdc2, was required
to trigger several key events in the cell-division cycle.
When that gene was inactivated by a mutation, the yeast
cells would not divide. And when the cells were provided with a normal copy of the gene, their ability to
reproduce was restored.
It’s obvious that replacing a faulty Cdc2 gene in S. pombe
with a functioning Cdc2 gene from the same yeast
should repair the damage and enable the cell to divide
normally. But what about using a similar cell-division
gene from a different organism? That’s the question the
Nurse team tackled next.
Next of kin
Saccharomyces cerevisiae is another kind of yeast and
is one of a handful of model organisms biologists have
chosen to study to expand their understanding of how
cells work. Also used to brew beer, S. cerevisiae divides
by forming a small bud that grows steadily until it separates from the mother cell (see Figures 1–13 and 1–31).
Although S. cerevisiae and S. pombe differ in their style of
division, both rely on a complex network of interacting
proteins to get the job done. But could the proteins from
one type of yeast substitute for those of the other?
To find out, Nurse and his colleagues prepared DNA
from healthy S. cerevisiae, and they introduced this DNA
into S. pombe cells that contained a mutation in the Cdc2
gene that kept the cells from dividing when the temperature was elevated. And they found that some of the
mutant S. pombe cells regained the ability to proliferate
when warm. If spread onto a culture plate containing
a growth medium, the rescued cells could divide again
and again to form visible colonies, each containing millions of individual yeast cells (Figure 1–35). Upon closer
examination, the researchers discovered that these “rescued” yeast cells had received a fragment of DNA that
contained the S. cerevisiae version of Cdc2—a gene that
had been discovered in pioneering studies of the cell
cycle by Lee Hartwell and colleagues.
The result was exciting, but perhaps not all that surprising. After all, how different can one yeast be from
another? A more demanding test would be to use DNA
from a more distant relative. So Nurse’s team repeated
the experiment, this time using human DNA. And the
results were the same. The human equivalent of the
Model Organisms
introduce
fragments of
foreign yeast DNA
(from S. cerevisiae)
spread cells over plate;
incubate at warm
temperature
mutant S. pombe cells
with a temperature-sensitive
Cdc2 gene cannot
divide at warm temperature
cells that received
a functional S. cerevisiae
substitute for the Cdc2 gene will
divide to form a colony
at the warm temperature
Figure 1–35 S. pombe mutants defective in a cell-cycle gene
can be rescued by the equivalent gene from S. cerevisiae.
DNA is collected from S. cerevisiae and broken into large
fragments, which are introduced into a culture of mutant
S. pombe cells dividing at room temperature. We discuss how
DNA can be manipulated and transferred into different cell types
in Chapter 10. These yeast cells are then spread onto a plate
containing a suitable growth medium and are incubated at a
warm temperature, at which the mutant Cdc2 protein is inactive.
The rare cells that survive
and proliferate on these plates have
ECB4 e1.36/1.34
been rescued by incorporation of a foreign gene that allows
them to divide normally at the higher temperature.
S. pombe Cdc2 gene could rescue the mutant yeast cells,
allowing them to divide normally.
Gene reading
This result was much more surprising—even to Nurse.
The ancestors of yeast and humans diverged some 1.5
billion years ago. So it was hard to believe that these
human
S. pombe
S. cerevisiae
31
two organisms would orchestrate cell division in such
a similar way. But the results clearly showed that the
human and yeast proteins are functionally equivalent.
Indeed, Nurse and colleagues demonstrated that the
proteins are almost exactly the same size and consist of
amino acids strung together in a very similar order; the
human Cdc2 protein is identical to the S. pombe Cdc2
protein in 63% of its amino acids and is identical to the
equivalent protein from S. cerevisiae in 58% of its amino
acids (Figure 1–36). Together with Tim Hunt, who discovered a different cell-cycle protein called cyclin, Nurse
and Hartwell shared a 2001 Nobel Prize for their studies
of key regulators of the cell cycle.
The Nurse experiments showed that proteins from very
different eukaryotes can be functionally interchangeable and suggested that the cell cycle is controlled in
a similar fashion in every eukaryotic organism alive
today. Apparently, the proteins that orchestrate the cycle
in eukaryotes are so fundamentally important that they
have been conserved almost unchanged over more than
a billion years of eukaryotic evolution.
The same experiment also highlights another, even more
basic, point. The mutant yeast cells were rescued, not by
direct injection of the human protein, but by introduction of a piece of human DNA. Thus the yeast cells could
read and use this information correctly, indicating that,
in eukaryotes, the molecular machinery for reading the
information encoded in DNA is also similar from cell to
cell and from organism to organism. A yeast cell has
all the equipment it needs to interpret the instructions
encoded in a human gene and to use that information to
direct the production of a fully functional human protein.
The story of Cdc2 is just one of thousands of examples of
how research in yeast cells has provided critical insights
into human biology. Although it may sound paradoxical, the shortest, most efficient path to improving human
health will often begin with detailed studies of the biology of simple organisms such as brewer’s or baker’s
yeast.
FGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKLPLFHGDSEIDQLFRIPRALGTPNNEVWPEVESLQDYKNTFP
FGLARSFGVPLRNYTHEIVTLWYRAPEVLLGSRHYSTGVDIWSVGCIFAENIRRSPLFPGDSEIDEIFKIPQVLGTPNEEVWPGVTLLQDYKSTFP
FGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEHCNRLPIFSGDSEIDQIFKIPRVLGTPNEAIWPDIVYLPDFKPSFP
Figure 1–36 The cell-division-cycle proteins from yeasts and human are very similar in their amino acid sequences. Identities
between the amino acid sequences of a region of the human Cdc2 protein and a similar region of the equivalent proteins in
S. pombe and S. cerevisiae are indicated by green shading. Each amino acid is represented by a single letter.
32
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–37 Zebrafish are popular models for studies of vertebrate
development. (A) These small, hardy, tropical fish are a staple in many
home aquaria. But they are also ideal for developmental studies, as their
transparent embryos (B) make it easy to observe cells moving and changing
their characters in the living organism as it develops. (A, courtesy of Steve
Baskauf; B, from M. Rhinn et al., Neural Dev. 4:12, 2009. With permission
from BioMed Central Ltd.)
creature is transparent for the first 2 weeks of its life, it provides an ideal
system in which to observe how cells behave during development in a
living animal (Figure 1–37).
(A)
(B)
1 cm
150 µm
ECB4 e1.39/1.37
Mammals are among the most complex of animals, and the mouse has
long been used as the model organism in which to study mammalian
genetics, development, immunology, and cell biology. Thanks to modern
molecular biological techniques, it is now possible to breed mice with
deliberately engineered mutations in any specific gene, or with artificially
constructed genes introduced into them. In this way, one can test what
a given gene is required for and how it functions. Almost every human
gene has a counterpart in the mouse, with a similar DNA sequence and
function. Thus, this animal has proven an excellent model for studying
genes that are important in both human health and disease.
Biologists Also Directly Study Human Beings and
Their Cells
Humans are not mice—or fish or flies or worms or yeast—and so we also
study human beings themselves. Like bacteria or yeast, our individual
cells can be harvested and grown in culture, where we can study their
biology and more closely examine the genes that govern their functions.
Given the appropriate surroundings, most human cells—indeed, most
cells from animals or plants—will survive, proliferate, and even express
specialized properties in a culture dish. Experiments using such cultured
cells are sometimes said to be carried out in vitro (literally, “in glass”) to
contrast them with experiments on intact organisms, which are said to be
carried out in vivo (literally, “in the living”).
Although not true for all types of cells, many types of cells grown in
culture display the differentiated properties appropriate to their origin:
fibroblasts, a major cell type in connective tissue, continue to secrete
collagen; cells derived from embryonic skeletal muscle fuse to form
muscle fibers, which contract spontaneously in the culture dish; nerve
cells extend axons that are electrically excitable and make synapses with
other nerve cells; and epithelial cells form extensive sheets, with many
of the properties of an intact epithelium (Figure 1–38). Because cultured
cells are maintained in a controlled environment, they are accessible to
study in ways that are often not possible in vivo. For example, cultured
cells can be exposed to hormones or growth factors, and the effects that
these signal molecules have on the shape or behavior of the cells can be
easily explored.
In addition to studying human cells in culture, humans are also examined directly in clinics. Much of the research on human biology has been
driven by medical interests, and the medical database on the human species is enormous. Although naturally occurring mutations in any given
human gene are rare, the consequences of many mutations are well documented. This is because humans are unique among animals in that they
report and record their own genetic defects: in no other species are billions of individuals so intensively examined, described, and investigated.
Nevertheless, the extent of our ignorance is still daunting. The mammalian body is enormously complex, being formed from thousands of
Model Organisms
(A)
(C)
(B)
20 mm
100 mm
billions of cells, and one might despair of ever understanding how the
DNA in a fertilized mouse egg cell makes it generate a mouse rather than
a fish, or how the DNA in a human egg cell directs the development of
a human rather than a mouse. Yet the revelations of molecular biology
ECB4
e4.48/1.38
have made the task seem eminently approachable.
As much
as anything,
this new optimism has come from the realization that the genes of one
type of animal have close counterparts in most other types of animals,
apparently serving similar functions (Figure 1–39). We all have a common evolutionary origin, and under the surface it seems that we share
the same molecular mechanisms. Flies, worms, fish, mice, and humans
thus provide a key to understanding how animals in general are made
and how their cells work.
100 mm
Figure 1–38 Cells in culture often display
properties that reflect their origin.
(A) Phase-contrast micrograph of fibroblasts
in culture. (B) Micrograph of cultured
myoblasts, some of which have fused
to form multinucleate muscle cells that
spontaneously contract in culture.
(C) Cultured epithelial cells forming a cell
sheet. Movie 1.7 shows a single heart
muscle cell beating in culture. (A, courtesy
of Daniel Zicha; B, courtesy of Rosalind
Zalin; C, from K.B. Chua et al., Proc. Natl
Acad. Sci. USA 104:11424–11429, 2007, with
permission from the National Academy of
Sciences.)
Comparing Genome Sequences Reveals Life’s Common
Heritage
At a molecular level, evolutionary change has been remarkably slow. We
can see in present-day organisms many features that have been preserved
through more than 3 billion years of life on Earth—about one-fifth of the
age of the universe. This evolutionary conservatism provides the foundation on which the study of molecular biology is built. To set the scene for
the chapters that follow, therefore, we end this chapter by considering a
little more closely the family relationships and basic similarities among
all living things. This topic has been dramatically clarified in the past few
years by technological advances that have allowed us to determine the
complete genome sequences of thousands of organisms, including our
own species (as discussed in more detail in Chapter 9).
The first thing we note when we look at an organism’s genome is its
overall size and how many genes it packs into that length of DNA.
Prokaryotes carry very little superfluous genetic baggage and, nucleotide-
Figure 1–39 Different species share
similar genes. The human baby and the
mouse shown here have similar white
patches on their foreheads because they
both have defects in the same gene (called
Kit ), which is required for the development
and maintenance of some pigment cells.
(Courtesy of R.A. Fleischman, from Proc.
Natl Acad. Sci. USA 88:10885–10889,
1991. With permission from the National
Academy of Sciences.)
33
34
Chapter 1
Cells: The Fundamental Units of Life
Figure 1–40 Organisms vary enormously
in the size of their genomes. Genome size
is measured in nucleotide pairs of DNA per
haploid genome, that is, per single copy
of the genome. (The body cells of sexually
reproducing organisms such as ourselves
are generally diploid: they contain two
copies of the genome, one inherited from
the mother, the other from the father.)
Closely related organisms can vary widely
in the quantity of DNA in their genomes (as
indicated by the length of the green bars),
even though they contain similar numbers
of functionally distinct genes. (Adapted from
T.R. Gregory, 2008, Animal Genome Size
Database: www.genomesize.com)
MAMMALS, BIRDS,REPTILES
AMPHIBIANS, FISHES
human
zebrafish
Drosophila
CRUSTACEANS, INSECTS
newt
shrimp
Caenorhabditis
NEMATODE WORMS
PLANTS, ALGAE
FUNGI
frog
Arabidopsis
wheat
yeast
malarial parasite
PROTOZOANS
E. coli
amoeba
BACTERIA
ARCHAEA
105
106
107
108
109
1010
nucleotide pairs per haploid genome
1011
1012
for-nucleotide, they squeeze a lot of information into their relatively small
genomes. E. coli, for example, carries its genetic instructions in a single, circular, double-stranded molecule of DNA that contains 4.6 million
nucleotide pairs and 4300 genes.
The
simplest known bacterium contains
ECB4
e1.41/1.40
only about 500 genes, but most prokaryotes have genomes that contain
at least 1 million nucleotide pairs and 1000–8000 genes. With these few
thousand genes, prokaryotes are able to thrive in even the most hostile
environments on Earth.
The compact genomes of typical bacteria are dwarfed by the genomes of
typical eukaryotes. The human genome, for example, contains about 700
times more DNA than the E. coli genome, and the genome of an amoeba
contains about 100 times more than ours (Figure 1–40). The rest of the
model organisms we have described have genomes that fall somewhere
in between E. coli and human in terms of size. S. cerevisiae contains about
2.5 times as much DNA as E. coli; Drosophila has about 10 times more
DNA per cell than yeast; and mice have about 20 times more DNA per cell
than the fruit fly (Table 1–2).
Table 1–2 Some Model Organisms and Their Genomes
Organism
Genome size*
(nucleotide pairs)
Approximate
number of genes
Homo sapiens
(human)
3200 × 106
30,000
Mus musculus
(mouse)
2800 × 106
30,000
Drosophila melanogaster
(fruit fly)
200 × 106
15,000
Arabidopsis thaliana
(plant)
220 × 106
29,000
Caenorhabditis elegans
(roundworm)
130 × 106
21,000
Saccharomyces cerevisiae
(yeast)
13 × 106
6600
Escherichia coli
(bacteria)
4.6 × 106
4300
*Genome size includes an estimate for the amount of highly repeated DNA sequence
not in genome databases.
Chapter 1 Essential Concepts
In terms of gene numbers, however, the differences are not so great. We
have only about six times as many genes as E. coli. Moreover, many of
our genes—and the proteins they encode—fall into closely related family groups, such as the family of hemoglobins, which has nine closely
related members in humans. Thus the number of fundamentally different
proteins in a human is not very many times more than in a bacterium,
and the number of human genes that have identifiable counterparts in the
bacterium is a significant fraction of the total.
This high degree of “family resemblance” is striking when we compare
the genome sequences of different organisms. When genes from different
organisms have very similar nucleotide sequences, it is highly probable
that both descended from a common ancestral gene. Such genes (and
their protein products) are said to be homologous. Now that we have the
complete genome sequences of many different organisms from all three
domains of life—archaea, bacteria, and eukaryotes—we can search systematically for homologies that span this enormous evolutionary divide.
By taking stock of the common inheritance of all living things, scientists
are attempting to trace life’s origins back to the earliest ancestral cells.
Genomes Contain More Than Just Genes
Although our view of genome sequences tends to be “gene-centric,” our
genomes contain much more than just genes. The vast bulk of our DNA
does not code for proteins or for functional RNA molecules. Instead, it
includes a mixture of sequences that help regulate gene activity, plus
sequences that seem to be dispensable. The large quantity of regulatory
DNA contained in the genomes of eukaryotic multicellular organisms
allows for enormous complexity and sophistication in the way different
genes are brought into action at different times and places. Yet, in the
end, the basic list of parts—the set of proteins that the cells can make, as
specified by the DNA—is not much longer than the parts list of an automobile, and many of those parts are common not only to all animals, but
also to the entire living world.
That DNA can program the growth, development, and reproduction of
living cells and complex organisms is truly amazing. In the rest of this
book, we will try to explain what is known about how cells work—by
examining their component parts, how these parts work together, and
how the genome of each cell directs the manufacture of the parts the cell
needs to function and to reproduce.
Essential Concepts
•
Cells are the fundamental units of life. All present-day cells are
believed to have evolved from an ancestral cell that existed more
than 3 billion years ago.
•
All cells are enclosed by a plasma membrane, which separates the
inside of the cell from its environment.
•
All cells contain DNA as a store of genetic information and use it to
guide the synthesis of RNA molecules and proteins.
•
Cells in a multicellular organism, though they all contain the same
DNA, can be very different. They turn on different sets of genes
according to their developmental history and to signals they receive
from their environment.
•
Animal and plant cells are typically 5–20 μm in diameter and can be
seen with a light microscope, which also reveals some of their internal components, including the larger organelles.
35
36
Chapter 1
Cells: The Fundamental Units of Life
•
The electron microscope reveals even the smallest organelles, but
specimens require elaborate preparation and cannot be viewed while
alive.
•
Specific large molecules can be located in fixed or living cells with a
fluorescence microscope.
•
The simplest of present-day living cells are prokaryotes: although
they contain DNA, they lack a nucleus and other organelles and probably resemble most closely the ancestral cell.
•
Different species of prokaryotes are diverse in their chemical
capabilities and inhabit an amazingly wide range of habitats. Two
fundamental evolutionary subdivisions are recognized: bacteria and
archaea.
•
Eukaryotic cells possess a nucleus and other organelles not found in
prokaryotes. They probably evolved in a series of stages, including
the acquisition of mitochondria by engulfment of aerobic bacteria
and (for plant cells) the acquisition of chloroplasts by engulfment of
photosynthetic bacteria.
•
The nucleus contains the genetic information of the eukaryotic
organism, stored in DNA molecules.
•
The cytoplasm includes all of the cell’s contents outside the nucleus
and contains a variety of membrane-enclosed organelles with specialized functions: mitochondria carry out the final oxidation of food
molecules; in plant cells, chloroplasts perform photosynthesis; the
endoplasmic reticulum and the Golgi apparatus synthesize complex
molecules for export from the cell and for insertion in cell membranes; lysosomes digest large molecules.
•
Outside the membrane-enclosed organelles in the cytoplasm is the
cytosol, a very concentrated mixture of large and small molecules
that carry out many essential biochemical processes.
•
The cytoskeleton is composed of protein filaments that extend
throughout the cytoplasm and are responsible for cell shape and
movement and for the transport of organelles and other large molecular complexes from one location to another.
•
Free-living, single-celled eukaryotic microorganisms are complex
cells that can swim, mate, hunt, and devour other microorganisms.
•
Animals, plants, and some fungi consist of diverse eukaryotic cell
types, all derived from a single fertilized egg cell; the number of such
cells cooperating to form a large multicellular organism such as a
human runs into thousands of billions.
•
Biologists have chosen a small number of model organisms to study
closely, including the bacterium E. coli, brewer’s yeast, a nematode
worm, a fly, a small plant, a fish, a mouse, and humans themselves.
•
The simplest known cell is a bacterium with about 500 genes, but
most cells contain significantly more. The human genome has about
25,000 genes, which is only about twice as many as a fly and six
times as many as E. coli.
Chapter 1 End-of-Chapter Questions
Key terms
archaeon
bacterium
cell
chloroplast
chromosome
cytoplasm
cytoskeleton
cytosol
DNA
electron microscope
eukaryote
nucleus
evolution
organelle
fluorescence microscope photosynthesis
genome
plasma membrane
homologous
prokaryote
micrometer
protein
microscope
protozoan
mitochondrion
ribosome
model organismRNA
Questions
Question 1–8
By now you should be familiar with the following cellular
components. Briefly define what they are and what function
they provide for cells.
H.Lysosomes and peroxisomes are the sites of degradation
of unwanted materials.
Question 1–10
G. chromosomes
To get a feeling for the size of cells (and to practice the use
of the metric system), consider the following: the human
brain weighs about 1 kg and contains about 1012 cells.
Calculate the average size of a brain cell (although we
know that their sizes vary widely), assuming that each cell is
entirely filled with water (1 cm3 of water weighs 1 g). What
would be the length of one side of this average-sized brain
cell if it were a simple cube? If the cells were spread out as a
thin layer that is only a single cell thick, how many pages of
this book would this layer cover?
H.Golgi apparatus
Question 1–11
I.
Identify the different organelles indicated with letters in the
electron micrograph of a plant cell shown below. Estimate
the length of the scale bar in the figure.
A. cytosol
B. cytoplasm
C. mitochondria
D. nucleus
E. chloroplasts
F. lysosomes
peroxisomes
J. plasma membrane
K. endoplasmic reticulum
L. cytoskeleton
Question 1–9
Which of the following statements are correct? Explain your
answers.
A.The hereditary information of a cell is passed on by its
proteins.
D
C
B
A
B. Bacterial DNA is found in the cytosol.
C.Plants are composed of prokaryotic cells.
D.All cells of the same organism have the same number of
chromosomes (with the exception of egg and sperm cells).
E.The cytosol contains membrane-enclosed organelles,
such as lysosomes.
? mm
F.The nucleus and mitochondria are surrounded by a
double membrane.
G.Protozoans are complex organisms with a set of
specialized cells that form tissues, such as flagella,
mouthparts, stinging darts, and leglike appendages.
Question 1–12
There are three major classes of filaments that make up the
cytoskeleton. What are they, and what are the differences in
ECB4 Q1.12
37
38
Chapter 1
Cells: The Fundamental Units of Life
their functions? Which cytoskeletal filaments would be most
plentiful in a muscle cell or in an epidermal cell making up
the outer layer of the skin? Explain your answers.
Question 1–13
Natural selection is such a powerful force in evolution
because cells with even a small proliferation advantage
quickly outgrow their competitors. To illustrate this process,
consider a cell culture that contains 1 million bacterial cells
that double every 20 minutes. A single cell in this culture
acquires a mutation that allows it to divide faster, with a
generation time of only 15 minutes. Assuming that there is
an unlimited food supply and no cell death, how long would
it take before the progeny of the mutated cell became
predominant in the culture? (Before you go through the
calculation, make a guess: do you think it would take about
a day, a week, a month, or a year?) How many cells of either
type are present in the culture at this time? (The number of
cells N in the culture at time t is described by the equation
N = N0 × 2t/G, where N0 is the number of cells at zero time
and G is the generation time.)
Question 1–14
When bacteria are grown under adverse conditions, i.e., in
the presence of a poison such as an antibiotic, most cells
grow and proliferate slowly. But it is not uncommon that the
growth rate of a bacterial culture kept in the presence of
the poison is restored after a few days to that observed in
its absence. Suggest why this may be the case.
Question 1–15
Apply the principle of exponential growth of a culture as
described in Question 1–13 to the cells in a multicellular
organism, such as yourself. There are about 1013 cells
in your body. Assume that one cell acquires a mutation
that allows it to divide in an uncontrolled manner (i.e., it
becomes a cancer cell). Some cancer cells can proliferate
with a generation time of about 24 hours. If none of the
cancer cells died, how long would it take before 1013 cells in
your body would be cancer cells? (Use the equation
N = N0 × 2t/G, with t, the time, and G, the length of each
generation. Hint: 1013 ≈ 243.)
Question 1–16
Discuss the following statement: “The structure and
function of a living cell are dictated by the laws of physics
and chemistry.”
Question 1–17
What, if any, are the advantages in being multicellular?
Question 1–18
Draw to scale the outline of two spherical cells, one a
bacterium with a diameter of 1 μm, the other an animal cell
with a diameter of 15 μm. Calculate the volume, surface
area, and surface-to-volume ratio for each cell. How
would the latter ratio change if you included the internal
membranes of the cell in the calculation of surface area
(assume internal membranes have 15 times the area of the
plasma membrane)? (The volume of a sphere is given by
4πr3/3 and its surface by 4πr2, where r is its radius.) Discuss
the following hypothesis: “Internal membranes allowed
bigger cells to evolve.”
Question 1–19
What are the arguments that all living cells evolved from
a common ancestor cell? Imagine the very early days of
evolution of life on Earth. Would you assume that the
primordial ancestor cell was the first and only cell to form?
Question 1–20
In Figure 1–25, proteins are blue, nucleic acids are pink,
lipids are yellow, and polysaccharides are green. Identify
the major organelles and other important cellular structures
shown in this slice through a eukaryotic cell.
Question 1–21
Looking at some pond water under the microscope, you
notice an unfamiliar rod-shaped cell about 200 μm long.
Knowing that some exceptional bacteria can be as big
as this or even bigger, you wonder whether your cell is a
bacterium or a eukaryote. How will you decide? If it is not a
eukaryote, how will you discover whether it is a bacterium
or an archaeon?
chapter TWO
2
Chemical Components of Cells
It is at first sight difficult to accept that living creatures are merely chemical systems. Their incredible diversity of form, their seemingly purposeful
behavior, and their ability to grow and reproduce all seem to set them
apart from the world of solids, liquids, and gases that chemistry normally
describes. Indeed, until the nineteenth century, it was widely believed
that animals contained a vital force—an “animus”—that was responsible
for their distinctive properties.
We now know that there is nothing in living organisms that disobeys
chemical or physical laws. However, the chemistry of life is indeed a
special kind. First, it is based overwhelmingly on carbon compounds,
the study of which is known as organic chemistry. Second, it depends
almost exclusively on chemical reactions that take place in a watery,
or aqueous, solution and in the relatively narrow range of temperatures
experienced on Earth. Third, it is enormously complex: even the simplest
cell is vastly more complicated in its chemistry than any other chemical
system known. Fourth, it is dominated and coordinated by collections of
enormous polymeric molecules—chains of chemical subunits linked endto-end—whose unique properties enable cells and organisms to grow
and reproduce and to do all the other things that are characteristic of life.
Finally, the chemistry of life is tightly regulated: cells deploy a variety of
mechanisms to make sure that all their chemical reactions occur at the
proper place and time.
Because chemistry lies at the heart of all biology, in this chapter, we briefly
survey the chemistry of the living cell. We will meet the molecules from
which cells are made and examine their structures, shapes, and chemical
properties. These molecules determine the size, structure, and functions
CHEMICAL BONDS
SMALL MOLECULES IN CELLS
MACROMOLECULES IN CELLS
40
Chapter 2
nucleus
Chemical Components of Cells
cloud of
orbiting
electrons
of living cells. By understanding how they interact, we can begin to see
how cells exploit the laws of chemistry and physics to survive, thrive, and
reproduce.
Chemical Bonds
Figure 2–1 An atom consists of a nucleus
surrounded by an electron cloud. The
dense, positively charged nucleus contains
most of the atom’s mass. The much lighter
and negatively charged electrons occupy
space around the nucleus, as governed
by the lawsECB4
of quantum
mechanics. The
E2.01/2.01
electrons are depicted as a continuous
cloud, as there is no way of predicting
exactly where an electron is at any given
instant. The density of shading of the cloud
is an indication of the probability that
electrons will be found there. The diameter
of the electron cloud ranges from about
0.1 nm (for hydrogen) to about 0.4 nm (for
atoms of high atomic number). The nucleus
is very much smaller: about 5 × 10–6 nm for
carbon, for example.
Matter is made of combinations of elements—substances such as hydrogen or carbon that cannot be broken down or interconverted by chemical
means. The smallest particle of an element that still retains its distinctive
chemical properties is an atom. The characteristics of substances other
than pure elements—including the materials from which living cells are
made—depend on which atoms they contain and the way these atoms
are linked together in groups to form molecules. To understand living
organisms, therefore, it is crucial to know how the chemical bonds that
hold atoms together in molecules are formed.
Cells Are Made of Relatively Few Types of Atoms
Each atom has at its center a dense, positively charged nucleus, which
is surrounded at some distance by a cloud of negatively charged electrons, held there by electrostatic attraction to the nucleus (Figure 2–1).
The nucleus consists of two kinds of subatomic particles: protons, which
are positively charged, and neutrons, which are electrically neutral. The
number of protons present in an atom’s nucleus determines its atomic
number. An atom of hydrogen has a nucleus composed of a single proton; so hydrogen, with an atomic number of 1, is the lightest element.
An atom of carbon has six protons in its nucleus and an atomic number
of 6 (Figure 2–2). The electric charge carried by each proton is exactly
equal and opposite to the charge carried by a single electron. Because
the whole atom is electrically neutral, the number of negatively charged
electrons surrounding the nucleus is equal to the number of positively
charged protons that the nucleus contains; thus the number of electrons
in an atom also equals the atomic number. All atoms of a given element have the same atomic number, and we will see shortly that it is this
number that dictates each atom’s chemical behavior.
Neutrons have essentially the same mass as protons. They contribute to
the structural stability of the nucleus—if there are too many or too few,
the nucleus may disintegrate by radioactive decay—but they do not alter
the chemical properties of the atom. Thus an element can exist in several
physically distinguishable but chemically identical forms, called isotopes, each having a different number of neutrons but the same number
of protons. Multiple isotopes of almost all the elements occur naturally,
Figure 2–2 The number of protons in
an atom determines its atomic number.
Schematic representations of an atom of
carbon and an atom of hydrogen are shown.
The nucleus of every atom except hydrogen
consists of both positively charged protons
and electrically neutral neutrons; the atomic
weight equals the number of protons plus
neutrons. The number of electrons in an
atom is equal to the number of protons, so
that the atom has no net charge. In contrast
to Figure 2–1, the electrons are shown
here as individual particles. The concentric
black circles represent in a highly schematic
form the “orbits” (that is, the different
distributions) of the electrons. The neutrons,
protons, and electrons are in reality minute
in relation to the atom as a whole; their size
is greatly exaggerated here.
neutron
electron
proton
+
+
+ +
+
+
+
carbon atom
hydrogen atom
atomic number = 6
atomic weight = 12
atomic number = 1
atomic weight = 1
Chemical Bonds
including some that are unstable—and thus radioactive. For example, while most carbon on Earth exists as the stable isotope carbon 12,
with six protons and six neutrons, also present are small amounts of an
unstable isotope, carbon 14, which has six protons and eight neutrons.
Carbon 14 undergoes radioactive decay at a slow but steady rate, which
allows archaeologists to estimate the age of organic material.
The atomic weight of an atom, or the molecular weight of a molecule,
is its mass relative to that of a hydrogen atom. This is essentially equal to
the number of protons plus neutrons that the atom or molecule contains,
because the electrons are so light that they contribute almost nothing to
the total mass. Thus the major isotope of carbon has an atomic weight
of 12 and is written as 12C. The unstable carbon isotope just mentioned
has an atomic weight of 14 and is written as 14C. The mass of an atom or
a molecule is generally specified in daltons, one dalton being an atomic
mass unit approximately equal to the mass of a hydrogen atom.
Atoms are so small that it is hard to imagine their size. An individual
carbon atom is roughly 0.2 nm in diameter, so that it would take about
5 million of them, laid out in a straight line, to span a millimeter. One
proton or neutron weighs approximately 1/(6 × 1023) gram. As hydrogen
has only one proton—thus an atomic weight of 1—1 gram of hydrogen
contains 6 × 1023 atoms. For carbon—which has six protons and six neutrons, and an atomic weight of 12—12 grams contain 6 × 1023 atoms. This
huge number, called Avogadro’s number, allows us to relate everyday
quantities of chemicals to numbers of individual atoms or molecules. If
a substance has a molecular weight of M, M grams of the substance will
contain 6 × 1023 molecules. This quantity is called one mole of the substance (Figure 2–3). The concept of mole is used widely in chemistry as
a way to represent the number of molecules that are available to participate in chemical reactions.
There are about 90 naturally occurring elements, each differing from the
others in the number of protons and electrons in its atoms. Living organisms, however, are made of only a small selection of these elements, four
of which—carbon (C), hydrogen (H), nitrogen (N), and oxygen (O)—constitute 96 % of an organism’s weight. This composition differs markedly
from that of the nonliving inorganic environment on Earth (Figure 2–4)
and is evidence of a distinctive type of chemistry.
The Outermost Electrons Determine How Atoms Interact
To understand how atoms come together to form the molecules that
make up living organisms, we have to pay special attention to the atoms’
electrons. Protons and neutrons are welded tightly to one another in an
atom’s nucleus, and they change partners only under extreme conditions—during radioactive decay, for example, or in the interior of the sun
or of a nuclear reactor. In living tissues, only the electrons of an atom
undergo rearrangements. They form the accessible part of the atom and
specify the rules of chemistry by which atoms combine to form molecules.
Electrons are in continuous motion around the nucleus, but motions on
this submicroscopic scale obey different laws from those we are familiar
with in everyday life. These laws dictate that electrons in an atom can
exist only in certain discrete regions of movement—roughly speaking,
in discrete orbits. Moreover, there is a strict limit to the number of electrons that can be accommodated in an orbit of a given type, a so-called
electron shell. The electrons closest on average to the positive nucleus
are attracted most strongly to it and occupy the inner, most tightly bound
shell. This innermost shell can hold a maximum of two electrons. The
second shell is farther away from the nucleus, and can hold up to eight
A mole is X grams of a substance,
where X is the molecular weight of the
substance. A mole will contain
23
6 × 10 molecules of the substance.
1 mole of carbon weighs 12 g
1 mole of glucose weighs 180 g
1 mole of sodium chloride weighs 58 g
A one molar solution has a
concentration of 1 mole of the substance
in 1 liter of solution. A 1 M solution of
glucose, for example, contains 180 g/l,
and a one millimolar (1 mM) solution
contains 180 mg/l.
The standard abbreviation for gram is g;
the abbreviation for liter is L.
Figure 2–3 What’s a mole? Some sample
calculations of moles and molar solutions.
ECB4 e2.03/2.03
41
Chapter 2
Chemical Components of Cells
Figure 2–4 The distribution of elements
in the Earth’s crust differs radically from
that in a living organism. The abundance
of each element is expressed here as a
percentage of the total number of atoms
present in a biological or geological sample,
including water. Thus, for example, more
than 60% of the atoms in the human body
are hydrogen atoms, and nearly 30% of the
atoms in the Earth’s crust are silicon atoms
(Si). The relative abundance of elements is
similar in all living things.
70
60
50
human body
40
Earth's crust
percent relative abundance
42
30
20
10
Question 2–1
A cup of water, containing exactly
18 g, or 1 mole, of water, was
emptied into the Aegean Sea
3000 years ago. What are the
chances that the same quantity
of water, scooped today from the
Pacific Ocean, would include at
least one of these ancient water
molecules? Assume perfect mixing
and an approximate volume for the
world’s oceans of 1.5 billion cubic
kilometers (1.5 × 109 km3).
H
C
O
N
Ca
and
Mg
Na
and
K
P
Al
Si
others
electrons. The third shell can also hold up to eight electrons, which are
even less tightly bound. The fourth and fifth shells can hold 18 electrons each. Atoms with more than four shells are very rare in biological
molecules.
The arrangement of electrons in an atom is most stable when all the
electrons are in the most tightly bound states that are possible for them—
that is, when they occupy the innermost shells, closest to the nucleus.
Therefore, with certain exceptions in the larger atoms, the electrons of an
atom fill the shells in order—the first before the second, the second before
the third, and so on. An atom whose outermost shell is entirely filled
with electrons is especially stable
and therefore chemically unreactive.
ECB4 e2.04/2.04
Examples are helium with 2 electrons (atomic number 2), neon with 2 + 8
electrons (atomic number 10), and argon with 2 + 8 + 8 electrons (atomic
number 18); these are all inert gases. Hydrogen, by contrast, has only
one electron, which leaves its outermost shell half-filled, so it is highly
reactive. The atoms found in living organisms all have outermost shells
that are incompletely filled, and they are therefore able to react with one
another to form molecules (Figure 2–5).
Because an incompletely filled electron shell is less stable than one that
is completely filled, atoms with incomplete outer shells have a strong
tendency to interact with other atoms so as to either gain or lose enough
electrons to achieve a completed outermost shell. This electron exchange
can be achieved either by transferring electrons from one atom to another
or by sharing electrons between two atoms. These two strategies generate the two types of chemical bonds that bind atoms to one another: an
ionic bond is formed when electrons are donated by one atom to another,
whereas a covalent bond is formed when two atoms share a pair of electrons (Figure 2–6).
Chemical Bonds
Figure 2–5 An element’s chemical
reactivity depends on how its outermost
electron shell is filled. All of the elements
commonly found in living organisms have
outermost shells that are not completely
filled with electrons (red) and can thus
participate in chemical reactions with other
atoms. Inert gases (yellow), in contrast, have
completely filled outermost shells and are
thus chemically unreactive.
atomic number
electron shell
element
1
Hydrogen (H)
2
Helium (He)
6
Carbon (C)
7
Nitrogen (N)
8
Oxygen (O)
I
II
III
IV
10 Neon (Ne)
11 Sodium (Na)
12 Magnesium (Mg)
15 Phosphorus (P)
16 Sulfur (S)
17 Chlorine (Cl)
18 Argon (Ar)
19 Potassium (K)
20 Calcium (Ca)
An H atom, which needs only one more electron to fill its only shell, genECB4 e2.05/2.05 one covalent bond with another
erally acquires it by sharing—forming
atom. The other most common elements in living cells—C, N, and O,
which have an incomplete second shell, and P and S, which have an
incomplete third shell (see Figure 2–5)—generally share electrons and
achieve a filled outer shell of eight electrons by forming several covalent
bonds. The number of electrons an atom must acquire or lose (either by
sharing or by transfer) to attain a filled outer shell determines the number
of bonds the atom can make.
Because the state of the outer electron shell determines the chemical
properties of an element, when the elements are listed in order of their
atomic number we see a periodic recurrence of elements with similar
properties: an element with, say, an incomplete second shell containing
one electron will behave in much the same way as an element that has
filled its second shell and has an incomplete third shell containing one
electron. The metals, for example, have incomplete outer shells with just
one or a few electrons, whereas, as we have just seen, the inert gases
have full outer shells. This arrangement gives rise to the periodic table of
the elements, outlined in Figure 2–7, which shows elements found in living organisms highlighted in color.
atoms
atoms
+
+
+
+
molecule
covalent bond
A carbon atom contains six protons
and six neutrons.
A. What are its atomic number and
atomic weight?
B. How many electrons does it
have?
C. How many additional electrons
must it add to fill its outermost
shell? How does this affect carbon’s
chemical behavior?
D. Carbon with an atomic weight of
14 is radioactive. How does it differ
in structure from nonradioactive
carbon? How does this difference
affect its chemical behavior?
+
TRANSFER OF
ELECTRON
SHARING OF
ELECTRONS
+
Question 2–2
+
+
positive
ion
negative
ion
ionic bond
Figure 2–6 Atoms can attain a more
stable arrangement of electrons in their
outermost shell by interacting with one
another. A covalent bond is formed when
electrons are shared between atoms. An
ionic bond is formed when electrons are
transferred from one atom to the other. The
two cases shown represent extremes; often,
covalent bonds form with a partial transfer
(unequal sharing of electrons), resulting in a
polar covalent bond, as we discuss shortly.
43
44
Chapter 2
Chemical Components of Cells
Figure 2–7 The chemistry of life is
predominantly the chemistry of lighter
elements. When ordered by their atomic
number into a periodic table, elements fall
into groups that show similar properties
based on the number of electrons each
element possesses in its outer shell. Atoms
in the same vertical column must gain or
lose the same number of electrons to attain
a filled outer shell, and they thus behave
similarly. Thus, both magnesium (Mg) and
calcium (Ca) tend to give away the two
electrons in their outer shells to form ionic
bonds with atoms such as chlorine (Cl) that
need extra electrons to complete their outer
shells.
The four elements highlighted in red
constitute 99% of the total number of atoms
present in the human body and about 96%
of our total weight. An additional seven
elements, highlighted in blue, together
represent about 0.9% of the total number
of atoms. Other elements, shown in green,
are required in trace amounts by humans.
It remains unclear whether those elements
shown in yellow are essential in humans
or not.
The atomic weights shown here are
those of the most common isotope of each
element.
two hydrogen atoms
+
+
+
TOO
CLOSE
(nuclei repel
each other)
+
+
+
+
+
bond length: 0.074 nm
hydrogen molecule
TOO
FAR
(no
attraction)
JUST
RIGHT
(covalent
bond)
atomic number
1
H
1
He
atomic weight
5
Li Be
11
19
K
39
Ca Sc
40
Rb Sr
Y
Ti
23
V
51
N
14
15
8
O
16
16
9
F
19
17
Ne
Ar
Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br
Kr
24
20
C
12
14
7
Cl
Al
Na Mg
23
B
11
12
6
24
52
42
25
55
26
56
27
59
28
59
29
64
Si
28
P
31
30
S
32
34
65
79
Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te
96
Cs Ba La
Hf Ta W Re Os
Fr Ra Ac
Rf Db
Ir
Pt Au Hg Tl Pb
35
53
I
127
Xe
Bi Po At Rn
Covalent Bonds Form by the Sharing of Electrons
All of the characteristics of a cell depend on the molecules it contains.
A molecule is a cluster of atoms held together by covalent bonds, in
which electrons are shared rather than transferred between atoms. The
shared electrons complete the
outer
shells of the interacting atoms. In the
ECB4
e2.07/2.07
simplest possible molecule—a molecule of hydrogen (H2)—two H atoms,
each with a single electron, share their electrons, thus filling their outermost shells. The shared electrons form a cloud of negative charge that
is densest between the two positively charged nuclei. This electron density helps to hold the nuclei together by opposing the mutual repulsion
between their positive charges that would otherwise force them apart.
The attractive and repulsive forces are in balance when the nuclei are
separated by a characteristic distance, called the bond length (Figure 2–8).
Whereas an H atom can form only a single covalent bond, the other common atoms that form covalent bonds in cells—O, N, S, and P, as well as
the all-important C—can form more than one. The outermost shells of
these atoms, as we have seen, can accommodate up to eight electrons,
and they form covalent bonds with as many other atoms as necessary to
reach this number. Oxygen, with six electrons in its outer shell, is most
stable when it acquires two extra electrons by sharing with other atoms,
and it therefore forms up to two covalent bonds. Nitrogen, with five outer
electrons, forms a maximum of three covalent bonds, while carbon, with
four outer electrons, forms up to four covalent bonds—thus sharing four
pairs of electrons (see Figure 2–5).
When one atom forms covalent bonds with several others, these multiple bonds have definite orientations in space relative to one another,
reflecting the orientations of the orbits of the shared electrons. Covalent bonds between multiple atoms are therefore characterized by specific bond angles, as well as by specific bond lengths and bond energies
(Figure 2–9). The four covalent bonds that can form around a carbon
Figure 2–8 The hydrogen molecule is held together by a covalent
bond. Each hydrogen atom in isolation has a single electron, which
means that its first (and only) electron shell is incompletely filled. By
coming together, the two atoms are able to share their electrons,
so that each obtains a completely filled first shell, with the shared
electrons adopting modified orbits around the two nuclei. The covalent
bond between the two atoms has a definite length—0.074 nm, which is
the distance between the two nuclei. If the atoms were closer together,
the positive nuclei would repel each other; if they were farther apart,
they would not be able to share electrons as effectively.
Chemical Bonds
O
(A)
oxygen
N
C
nitrogen
carbon
water (H2O)
(B)
propane (CH3-CH2-CH3)
Figure 2–9 Covalent bonds are
characterized by particular geometries.
(A) The spatial arrangement of the covalent
bonds that can be formed by oxygen,
nitrogen, and carbon. (B) Molecules formed
from these atoms therefore have a precise
three-dimensional structure defined by the
bond angles and bond lengths for each
covalent linkage. A water molecule, for
example, forms a “V” shape with an angle
close to 109°.
In these ball-and-stick models, the
different colored balls represent different
atoms, and the sticks represent the
covalent bonds. The colors traditionally
used to represent the different atoms—
black for carbon, white for hydrogen, blue
for nitrogen, and red for oxygen—were
established by the chemist August Wilhelm
Hofmann in 1865, when he used a set of
colored croquet balls to build molecular
models for a public lecture on “the
combining power of atoms.”
atom, for example, are arranged as if pointing to the four corners of a regular tetrahedron. The precise
orientation of the covalent bonds around
ECB4 e2.10/2.09
carbon produces the three-dimensional geometry of organic molecules.
There Are Different Types of Covalent Bonds
Most covalent bonds involve the sharing of two electrons, one donated
by each participating atom; these are called single bonds. Some covalent
bonds, however, involve the sharing of more than one pair of electrons.
Four electrons can be shared, for example, two coming from each participating atom; such a bond is called a double bond. Double bonds are
shorter and stronger than single bonds and have a characteristic effect
on the three-dimensional geometry of molecules containing them. A single covalent bond between two atoms generally allows the rotation of
one part of a molecule relative to the other around the bond axis. A double bond prevents such rotation, producing a more rigid and less flexible
arrangement of atoms (Figure 2–10). This restriction has a major influence on the three-dimensional shape of many macromolecules. Panel
2–1 (pp. 66–67) reviews the covalent bonds commonly encountered in
biological molecules.
Some molecules contain atoms that share electrons in a way that produces bonds that are intermediate in character between single and double
bonds. The highly stable benzene molecule, for example, is made up of
a ring of six carbon atoms in which the bonding electrons are evenly
distributed (although the arrangement is sometimes depicted as an alternating sequence of single and double bonds, as shown in Panel 2–1).
When the atoms joined by a single covalent bond belong to different elements, the two atoms usually attract the shared electrons to different
degrees. Covalent bonds in which the electrons are shared unequally in
this way are known as polar covalent bonds. A polar structure (in the electrical sense) is one in which the positive charge is concentrated toward
one end of the molecule (the positive pole) and the negative charge is
concentrated toward the other end (the negative pole). Oxygen and nitrogen atoms, for example, attract electrons relatively strongly, whereas an
H atom attracts electrons relatively weakly (because of the relative differences in the positive charges of the nuclei of C, O, N, and H). Thus the
(A) ethane
(B) ethene
Figure 2–10 Carbon–carbon double
bonds are shorter and more rigid than
carbon–carbon single bonds. (A) The
ethane molecule, with a single covalent
ECB4the
e2.11/2.10
bond between
two carbon atoms, shows
the tetrahedral arrangement of the three
single covalent bonds between each carbon
atom and its three attached H atoms. The
CH3 groups, joined by a covalent C–C
bond, can rotate relative to one another
around the bond axis. (B) The double
bond between the two carbon atoms in a
molecule of ethene (ethylene) alters the
bond geometry of the carbon atoms and
brings all the atoms into the same plane;
the double bond prevents the rotation of
one CH2 group relative to the other.
45
46
Chapter 2
Chemical Components of Cells
δ–
δ+
O
H
H
δ+
O
water
O
oxygen
Figure 2–11 In polar covalent bonds, the electrons are shared
unequally. Comparison of electron distributions in the polar covalent
bonds in a molecule of water (H2O) and the nonpolar covalent bonds
in a molecule of oxygen (O2). In H2O, electrons are more strongly
attracted to the oxygen nucleus than to the H nucleus, as indicated
by the distributions of the partial negative (δ–) and partial positive (δ+)
charges.
covalent bond between O and H, O–H, or between N and H, N–H, is polar
(Figure 2–11). An atom of C and an atom of H, by contrast, attract electrons more equally. Thus the bond between carbon and hydrogen, C–H,
is relatively nonpolar.
Covalent Bonds Vary in Strength
Question 2–3
ECB4 e2.12/2.11
Discuss whether the following
statement is correct: “An ionic
bond can, in principle, be thought
of as a very polar covalent bond.
Polar covalent bonds, then, fall
somewhere between ionic bonds
at one end of the spectrum and
nonpolar covalent bonds at the
other end.”
We have already seen that the covalent bond between two atoms has
a characteristic length that depends on the atoms involved. A further
crucial property of any chemical bond is its strength. Bond strength is
measured by the amount of energy that must be supplied to break the
bond, usually expressed in units of either kilocalories per mole (kcal/
mole) or kilojoules per mole (kJ/mole). A kilocalorie is the amount of
energy needed to raise the temperature of 1 liter of water by 1°C. Thus, if
1 kilocalorie of energy must be supplied to break 6 × 1023 bonds of a specific type (that is, 1 mole of these bonds), then the strength of that bond is
1 kcal/mole. One kilocalorie is equal to about 4.2 kJ, which is the unit of
energy universally employed by physical scientists and, increasingly, by
cell biologists as well.
To get an idea of what bond strengths mean, it is helpful to compare
them with the average energies of the impacts that molecules continually
undergo owing to collisions with other molecules in their environment—
their thermal, or heat, energy. Typical covalent bonds are stronger than
these thermal energies by a factor of 100, so they are resistant to being
pulled apart by thermal motions. In living organisms, they are normally
broken only during specific chemical reactions that are carefully controlled by highly specialized protein catalysts, called enzymes.
When water is present, covalent bonds are much stronger than ionic
bonds. In ionic bonds, electrons are transferred rather than shared, as
we now discuss.
Ionic Bonds Form by the Gain and Loss of Electrons
Ionic bonds are usually formed between atoms that can attain a completely filled outer shell most easily by donating electrons to—or accepting
electrons from—another atom, rather than by sharing them. For example,
returning to Figure 2–5, we see that a sodium (Na) atom can achieve a
filled outer shell by giving up the single electron in its third shell. By contrast, a chlorine (Cl) atom can complete its outer shell by gaining just one
electron. Consequently, if a Na atom encounters a Cl atom, an electron
can jump from the Na to the Cl, leaving both atoms with filled outer shells.
The offspring of this marriage between sodium, a soft and intensely reactive metal, and chlorine, a toxic green gas, is table salt (NaCl).
When an electron jumps from Na to Cl, both atoms become electrically charged ions. The Na atom that lost an electron now has one less
electron than it has protons in its nucleus; it therefore has a net single
positive charge (Na+). The Cl atom that gained an electron now has one
more electron than it has protons and has a net single negative charge
(Cl–). Because of their opposite charges, the Na+ and Cl– ions are attracted
Chemical Bonds
sodium atom (Na)
chlorine atom (Cl)
chloride ion (Cl–)
sodium chloride (NaCl)
(A)
(B)
sodium ion (Na+)
(C)
Figure 2–12 Sodium chloride is held
together by ionic bonds. (A) An atom
of sodium (Na) reacts with an atom of
chlorine (Cl). Electrons of each atom are
shown in their different shells; electrons
in the chemically reactive (incompletely
filled) outermost shells are shown in red.
The reaction takes place with transfer of a
single electron from sodium to chlorine,
forming two electrically charged atoms, or
ions, each with complete sets of electrons
in their outermost shells. The two ions have
opposite charge and are held together by
electrostatic attraction. (B) The product of
the reaction between sodium and chlorine,
crystalline sodium chloride, contains sodium
and chloride ions packed closely together
in a regular array in which the charges are
exactly balanced. (C) Color photograph of
crystals of sodium chloride.
1 mm
to each other and are thereby held together by an ionic bond (Figure
2–12A). Ions held together solely by ionic bonds are generally called salts
rather than molecules. A NaCl crystal contains astronomical numbers of
Na+ and Cl– packed together in a precise three-dimensional array with
E2.08/2.12
their opposite charges exactlyECB4
balanced:
a crystal only 1 mm across con19
tains about 2 × 10 ions of each type (Figure 2–12B and C).
Because of the favorable interaction between ions and water molecules
(which are polar), many salts (including NaCl) are highly soluble in water.
They dissociate into individual ions (such as Na+ and Cl–), each surrounded by a group of water molecules. Positive ions are called cations,
and negative ions are called anions. Small inorganic ions such as Na+, Cl–,
K+, and Ca2+ play important parts in many biological processes, including
the electrical activity of nerve cells, as we discuss in Chapter 12.
Noncovalent Bonds Help Bring Molecules Together
in Cells
In aqueous solution, ionic bonds are 10–100 times weaker than the covalent bonds that hold atoms together in molecules. But this weakness has
its place: much of biology depends on specific but transient interactions
between one molecule and another. These associations are mediated by
noncovalent bonds. Although noncovalent bonds are individually quite
weak, their energies can sum to create an effective force between two
molecules.
The ionic bonds that hold together the Na+ and Cl– ions in a salt crystal
(see Figure 2–12) are a form of noncovalent bond called an electrostatic
attraction. Electrostatic attractions are strongest when the atoms involved
are fully charged, as are Na+ and Cl–. But a weaker electrostatic attraction
also occurs between molecules that contain polar covalent bonds (see
Figure 2–11). Polar covalent bonds are thus extremely important in biology because they allow molecules to interact through electrical forces.
Any large molecule with many polar groups will have a pattern of partial positive and negative charges on its surface. When such a molecule
encounters a second molecule with a complementary set of charges,
the two will be attracted to each other by electrostatic attraction—even
Question 2–4
What, if anything, is wrong with
the following statement: “When
NaCl is dissolved in water, the
water molecules closest to the ions
will tend to preferentially orient
themselves so that their oxygen
atoms face the sodium ions and
face away from the chloride ions”?
Explain your answer.
47
48
Chapter 2
Chemical Components of Cells
though water greatly reduces the attractiveness of these charges in most
biological settings. When present in large numbers, however, weak noncovalent bonds on the surfaces of large molecules can promote strong
and specific binding (Figure 2–13).
Hydrogen Bonds Are Important Noncovalent Bonds For
Many Biological Molecules
Water accounts for about 70% of a cell’s weight, and most intracellular
reactions occur in an aqueous environment. Life on Earth is thought to
have begun in the ocean. Thus the properties of water have put a permanent stamp on the chemistry of living things.
Figure 2–13 A large molecule, such as
a protein, can bind to another protein
through complementary charges on the
surface of each molecule. In the aqueous
environment of a cell, the many individual
electrostatic attractions shown would help
the two proteins stay bound to each other.
ECB4 e2.13/2.13
In each molecule of water (H2O), the two H atoms are linked to the O
atom by covalent bonds. The two H–O bonds are highly polar because
the O is strongly attractive for electrons, whereas the H is only weakly
attractive. Consequently, there is an unequal distribution of electrons in
a water molecule, with a preponderance of positive charge on the two H
atoms and negative charge on the O (see Figure 2–11). When a positively
charged region of one water molecule (that is, one of its H atoms) comes
close to a negatively charged region (that is, the O) of a second water
molecule, the electrical attraction between them can establish a weak
bond called a hydrogen bond (Figure 2–14). These bonds are much
weaker than covalent bonds and are easily broken by random thermal
motions. Thus each bond lasts only an exceedingly short time. But the
combined effect of many weak bonds is far from trivial. Each water molecule can form hydrogen bonds through its two H atoms to two other
water molecules, producing a network in which hydrogen bonds are
being continually broken and formed. It is because of these interlocking
hydrogen bonds that water at room temperature is a liquid—with a high
boiling point and high surface tension—and not a gas. Without hydrogen bonds, life as we know it could not exist. The biologically significant
properties of water are reviewed in Panel 2–2 (pp. 68–69).
Hydrogen bonds are not limited to water. In general, a hydrogen bond
can form whenever a positively charged H atom held in one molecule
by a polar covalent linkage comes close to a negatively charged atom—
typically an oxygen or a nitrogen—belonging to another molecule (see
Figure 2–14). Hydrogen bonds can also occur between different parts of
a single large molecule, where they often help the molecule fold into a
particular shape. The length and strength of hydrogen bonds and of ionic
bonds are compared to those of covalent bonds in Table 2–1.
Molecules, such as alcohols, that contain polar bonds and that can form
hydrogen bonds mix well with water. As mentioned previously, molecules
carrying positive or negative charges (ions) likewise dissolve readily in
water. Such molecules are termed hydrophilic, meaning that they are
δ+
δ+
H
H
δ
O
H
δ+
_
TABLE 2–1 LENGTH AND STRENGTH OF SOME CHEMICAL BONDS
δ+
H
O
δ
_
hydrogen bond
Figure 2–14 A hydrogen bond can form
between two water molecules. These
bonds are largely responsible for water’s lifesustaining properties—including its ability
to exist as a liquid at the temperatures
inside the typical mammalian body.
Bond type
Length* (nm)
Strength (kcal/mole)
in vacuum
in water
Covalent
0.10
90 [377]**
90 [377]
Noncovalent: ionic bond
0.25
80 [335]
3 [12.6]
Noncovalent: hydrogen bond
0.17
4 [16.7]
1 [4.2]
*The bond lengths and strengths listed are approximate, because the exact values
will depend on the atoms involved.
**Values in brackets are kJ/mole. 1 calorie = 4.184 joules.
Chemical Bonds
“water-loving.” A large proportion of the molecules in the aqueous environment of a cell fall into this category, including sugars, DNA, RNA, and
a majority of proteins. Hydrophobic (“water-fearing”) molecules, by contrast, are uncharged and form few or no hydrogen bonds, and they do not
dissolve in water.
Hydrocarbons are important hydrophobic cell constituents (see Panel
2–1, pp. 66–67). In these molecules, the H atoms are covalently linked
to C atoms by nonpolar bonds. Because the H atoms have almost no net
positive charge, they cannot form effective hydrogen bonds to other molecules. This makes the hydrocarbon as a whole hydrophobic—a property
that is exploited by cells, whose membranes are constructed largely from
lipid molecules that have long hydrocarbon tails. Because lipids do not
dissolve in water, they can form the thin membrane barriers that keep
the aqueous interior of the cell separate from the surrounding aqueous
environment, as we discuss later.
Some Polar Molecules Form Acids and Bases in Water
One of the simplest kinds of chemical reaction, and one that has profound
significance in cells, takes place when a molecule possessing a highly
polar covalent bond between a hydrogen and another atom dissolves in
water. The hydrogen atom in such a bond has given up its electron almost
entirely to the companion atom, so it exists as an almost naked positively
charged hydrogen nucleus—in other words, a proton (H+). When the polar
molecule becomes surrounded by water molecules, the proton will be
attracted to the partial negative charge on the oxygen atom of an adjacent water molecule (see Figure 2–11); this proton can dissociate from
its original partner and associate instead with the oxygen atom of the
water molecule, generating a hydronium ion (H3O+) (Figure 2–15A). The
reverse reaction also takes place very readily, so one has to imagine an
equilibrium state in which billions of protons are constantly flitting to and
fro between one molecule and another in an aqueous solution.
Substances that release protons when they dissolve in water, thus forming H3O+, are termed acids. The higher the concentration of H3O+, the
more acidic the solution. H3O+ is present even in pure water, at a concentration of 10–7 M, as a result of the movement of protons from one water
molecule to another (Figure 2–15B). By tradition, the H3O+ concentration
polar
O covalent
CH3
bond
+
C
O–
δ
H+
δ
acetic acid
O
H
CH3
O
H
+
C
H
O
water
acetate
ion
(A)
H
O
+
H
hydronium
ion
hydrogen bond
H
H
(B)
O
H
H O
H
H2O
H2O
proton moves
from one H2O
molecule to
the other
O H
H +
H3O
+
hydronium
ion
+
O
H
–
OH
hydroxyl
ion
Figure 2–15 Protons move continuously from one water molecule to another
in aqueous solutions. (A) The reaction that takes place when a molecule of acetic
acid dissolves in water. At pH 7, nearly all of the acetic acid molecules are present as
acetate ions. (B) Water molecules are continually exchanging protons with each other
to form hydronium and hydroxyl ions. These ions in turn rapidly recombine to form
water molecules.
49
50
Chapter 2
Chemical Components of Cells
is usually referred to as the H+ concentration, even though most protons
in an aqueous solution are present as H3O+. To avoid the use of unwieldy
numbers, the concentration of H+ is expressed using a logarithmic scale
called the pH scale, as illustrated in Panel 2–2. Pure water has a pH of
7.0 and is thus neutral—that is, neither acidic (pH < 7) nor basic (pH > 7).
Acids are characterized as being strong or weak, depending on how readily they give up their protons to water. Strong acids, such as hydrochloric
acid (HCl), lose their protons easily. Acetic acid, on the other hand, is a
weak acid because it holds on to its proton more tightly when dissolved
in water. Many of the acids important in the cell—such as molecules
containing a carboxyl (COOH) group—are weak acids (see Panel 2–2, pp.
68–69). Their tendency to give up a proton with some reluctance is a useful characteristic, as it renders the molecules sensitive to changes in pH
in the cell—a property that can be exploited to regulate function.
Because protons can be passed readily to many types of molecules in
cells, thus altering the molecules’ character, the H+ concentration inside
a cell (the pH) must be closely controlled. Acids—especially weak acids—
will give up their protons more readily if the H+ concentration is low and
will tend to accept them back if the concentration is high.
Question 2–5
A. Are there any H3O+ ions
present in pure water at neutral pH
(i.e., at pH = 7.0)? If so, how are
they formed?
B. If they exist, what is the ratio
of H3O+ ions to H2O molecules at
neutral pH? (Hint: the molecular
weight of water is 18, and 1 liter
of water weighs 1 kg.)
The opposite of an acid is a base, which includes any molecule that
accepts a proton when dissolved in water. Just as the defining property
of an acid is that it raises the concentration of H3O+ ions by donating a
proton to a water molecule, so the defining property of a base is that it
raises the concentration of hydroxyl (OH–) ions by removing a proton
from a water molecule. Thus sodium hydroxide (NaOH) is basic (the term
alkaline is also used) because it dissociates in aqueous solution to form
Na+ ions and OH– ions; because it does so readily, NaOH is called a strong
base. Weak bases—which have a weak tendency to accept a proton from
water—however, are actually more important in cells. Many biologically
important weak bases contain an amino (NH2) group, which can generate OH– by taking a proton from water: –NH2 + H2O → –NH3+ + OH– (see
Panel 2–2, pp. 68–69).
Because an OH– ion combines with a proton to form a water molecule,
an increase in the OH– concentration forces a decrease in the H+ concentration, and vice versa. A pure solution of water thus contains an
equal concentration (10–7 M) of both ions, rendering it neutral (pH 7). The
interior of a cell is also kept close to neutral by the presence of buffers:
mixtures of weak acids and bases that can adjust proton concentrations
around pH 7 by releasing protons (acids) or taking them up (bases). This
give-and-take keeps the pH of the cell relatively constant under a variety
of conditions.
SMALL Molecules in Cells
Having looked at the ways atoms combine to form small molecules and
how these molecules behave in an aqueous environment, we now examine the main classes of small molecules found in cells and their biological
roles. Amazingly, we will see that a few basic categories of molecules,
formed from a handful of different elements, give rise to all the extraordinary richness of form and behavior displayed by living things.
A Cell Is Formed from Carbon Compounds
If we disregard water, nearly all the molecules in a cell are based on carbon. Carbon is outstanding among all the elements in its ability to form
large molecules; silicon—an element with the same number of electrons
in its outer shell—is a poor second. Because a carbon atom is small and
Small Molecules in Cells
has four electrons and four vacancies in its outer shell, it can form four
covalent bonds with other atoms (see Figure 2–9). Most importantly, one
carbon atom can join to other carbon atoms through highly stable covalent C–C bonds to form chains and rings and hence generate large and
complex molecules with no obvious upper limit to their size. The small
and large carbon compounds made by cells are called organic molecules. By contrast, all other molecules, including water, are said to be
inorganic.
Certain combinations of atoms, such as the methyl (–CH3), hydroxyl
(–OH), carboxyl (–COOH), carbonyl (–C=O), phosphoryl (–PO32–), and
amino (–NH2) groups, occur repeatedly in organic molecules. Each such
chemical group has distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs, including
whether the molecule tends to gain or lose protons and with which other
molecules it will interact. Knowing these groups and their chemical properties greatly simplifies understanding the chemistry of life. The most
common chemical groups and some of their properties are summarized
in Panel 2–1 (pp. 67–68).
Cells Contain Four Major Families of Small Organic
Molecules
The small organic molecules of the cell are carbon compounds with
molecular weights in the range 100–1000 that contain up to 30 or so
carbon atoms. They are usually found free in solution in the cytosol and
have many different roles. Some are used as monomer subunits to construct the cell’s giant polymeric macromolecules—its proteins, nucleic
acids, and large polysaccharides. Others serve as energy sources, which
are broken down and transformed into other small molecules in a maze
of intracellular metabolic pathways. Many have more than one role in the
cell—acting, for example, as both a potential subunit for a macromolecule and as an energy source. The small organic molecules are much less
abundant than the organic macromolecules, accounting for only about
one-tenth of the total mass of organic matter in a cell. As a rough guess,
there may be a thousand different kinds of these small organic molecules
in a typical animal cell.
All organic molecules are synthesized from—and are broken down
into—the same set of simple compounds. Both their synthesis and their
breakdown occur through sequences of simple chemical changes that
are limited in variety and follow step-by-step rules. As a consequence,
the compounds in a cell are chemically related, and most can be classified into a small number of distinct families. Broadly speaking, cells
contain four major families of small organic molecules: the sugars, the
fatty acids, the amino acids, and the nucleotides (Figure 2–16). Although
many compounds present in cells do not fit into these categories, these
four families of small organic molecules, together with the macromolecules made by linking them into long chains, account for a large fraction
of a cell’s mass (Table 2–2).
small organic building blocks
of the cell
larger organic molecules
of the cell
SUGARS
POLYSACCHARIDES, GLYCOGEN,
AND STARCH (IN PLANTS)
FATTY ACIDS
FATS AND MEMBRANE LIPIDS
AMINO ACIDS
PROTEINS
NUCLEOTIDES
NUCLEIC ACIDS
Figure 2–16 Sugars, fatty acids, amino
acids, and nucleotides are the four main
families of small organic molecules
in cells. They form the monomeric
building blocks, or subunits, for larger
organic molecules, including most of the
macromolecules and other molecular
assemblies of the cell. Some, like the sugars
and the fatty acids, are also energy sources.
51
52
Chapter 2
Chemical Components of Cells
TABLE 2–2 THE CHEMICAL COMPOSITION OF A BACTERIAL CELL
Percent of
total cell
weight
Approximate number
of types of each class
of molecule
Water
70
1
Inorganic ions
1
20
Sugars and precursors
1
250
Amino acids and precursors
0.4
100
Nucleotides and precursors
0.4
100
Fatty acids and precursors
1
50
Other small molecules
0.2
300
Phospholipids
2
4*
Macromolecules (nucleic acids,
proteins, and polysaccharides)
24
3000
*There are four classes of phospholipids, each of which exists in many varieties.
Sugars Are Both Energy Sources and Subunits of
Polysaccharides
Figure 2–17 The structure of glucose,
a monosaccharide, can be represented
in several ways. (A) A structural formula
in which the atoms are shown as chemical
symbols, linked together by solid lines
representing the covalent bonds. The
thickened lines are used to indicate the
plane of the sugar ring and to show that
the –H and –OH groups are not in the
same plane as the ring. (B) Another kind
of structural formula that shows the threedimensional structure of glucose in the
so-called “chair configuration.”
(C) A ball-and-stick model in which the
three-dimensional arrangement of the
atoms in space is indicated. (D) A spacefilling model, which, as well as depicting
the three-dimensional arrangement of the
atoms, also gives some idea of their relative
sizes and of the surface contours of the
molecule (Movie 2.1). The atoms in (C) and
(D) are colored as in Figure 2–9: C, black; H,
white; O, red. This is the conventional color
coding for these atoms and will be used
throughout this book.
The simplest sugars—the monosaccharides—are compounds with the
general formula (CH2O)n, where n is usually 3, 4, 5, or 6. Sugars, and the
larger molecules made from them, are also called carbohydrates because
of this simple formula. Glucose, for example, has the formula C6H12O6
(Figure 2–17). The formula, however, does not fully define the molecule:
the same set of carbons, hydrogens, and oxygens can be joined together
by covalent bonds in a variety of ways, creating structures with different
shapes. Thus glucose can be converted into a different sugar—mannose
or galactose—simply by switching the orientations of specific –OH groups
relative to the rest of the molecule (Panel 2–3, pp. 70–71). Each of these
sugars, moreover, can exist in either of two forms, called the d-form and
the l-form, which are mirror images of each other. Sets of molecules with
the same chemical formula but different structures are called isomers, and
mirror-image pairs of such molecules are called optical isomers. Isomers
are widespread among organic molecules in general, and they play a
CH2OH
H
C
HO
C
H
O
OH
H
C
C
H
OH
H
OH
HO
H
C
H
HO
(B)
(A)
(C)
CH2OH
(D)
H
H
O
OH
OH
H
53
Small Molecules in Cells
major part in generating the enormous variety of sugars. A more complete outline of sugar structures and chemistry is presented in Panel 2–3.
Monosaccharides can be linked by covalent bonds—called glycosidic
bonds—to form larger carbohydrates. Two monosaccharides linked
together make a disaccharide, such as sucrose, which is composed of
a glucose and a fructose unit. Larger sugar polymers range from the oligosaccharides (trisaccharides, tetrasaccharides, and so on) up to giant
polysaccharides, which can contain thousands of monosaccharide units.
In most cases, the prefix oligo- is used to refer to molecules made of a
small number of monomers, typically 2 to 10 in the case of oligosaccharides. Polymers, in contrast, can contain hundreds or thousands of
subunits.
The way sugars are linked together illustrates some common features of
biochemical bond formation. A bond is formed between an –OH group
on one sugar and an –OH group on another by a condensation reaction,
in which a molecule of water is expelled as the bond is formed. The subunits in other biological polymers, including nucleic acids and proteins,
are also linked by condensation reactions in which water is expelled. The
bonds created by all of these condensation reactions can be broken by
the reverse process of hydrolysis, in which a molecule of water is consumed (Figure 2–18).
Because each monosaccharide has several free hydroxyl groups that can
form a link to another monosaccharide (or to some other compound),
sugar polymers can be branched, and the number of possible polysaccharide structures is extremely large. For this reason, it is much more
difficult to determine the arrangement of sugars in a complex polysaccharide than to determine the nucleotide sequence of a DNA molecule or
the amino acid sequence of a protein, in which each unit is joined to the
next in exactly the same way.
The monosaccharide glucose has a central role as an energy source for
cells. It is broken down to smaller molecules in a series of reactions,
releasing energy that the cell can harness to do useful work, as we
explain in Chapter 13. Cells use simple polysaccharides composed only
of glucose units—principally glycogen in animals and starch in plants—as
long-term stores of glucose, held in reserve for energy production.
Sugars do not function exclusively in the production and storage of
energy. They are also used, for example, to make mechanical supports.
The most abundant organic molecule on Earth—the cellulose that forms
plant cell walls—is a polysaccharide of glucose. Another extraordinarily
abundant organic substance, the chitin of insect exoskeletons and fungal
cell walls, is also a polysaccharide—in this case, a linear polymer of a
sugar derivative called N-acetylglucosamine (see Panel 2–3, pp. 70–71).
Other polysaccharides, which tend to be slippery when wet, are the main
components of slime, mucus, and gristle.
Smaller oligosaccharides can be covalently linked to proteins to form
glycoproteins, or to lipids to form glycolipids (Panel 2–4, pp. 72–73), which
are both found in cell membranes. The sugar side chains attached to
glycoproteins and glycolipids in the plasma membrane are thought to
help protect the cell surface and often help cells adhere to one another.
Differences in the types of cell-surface sugars form the molecular basis
for different human blood groups.
Fatty Acid Chains Are Components of Cell Membranes
A fatty acid molecule, such as palmitic acid, has two chemically distinct
regions. One is a long hydrocarbon chain, which is hydrophobic and
not very reactive chemically. The other is a carboxyl (–COOH) group,
O
O
+
OH
HO
monosaccharide
monosaccharide
CONDENSATION
HYDROLYSIS
H2O
H2O
water expelled
water consumed
O
O
O
glycosidic
bond
disaccharide
Figure 2–18 Two monosaccharides can
be linked by a covalent glycosidic bond
to form a disaccharide. This reaction
E2.17/2.17
belongs ECB4
to a general
category of reactions
termed condensation reactions, in which
two molecules join together as a result of
the loss of a water molecule. The reverse
reaction (in which water is added) is termed
hydrolysis.
54
Chapter 2
Chemical Components of Cells
Figure 2–19 Fatty acids have both
hydrophobic and hydrophilic components.
The hydrophobic hydrocarbon chain is
attached to a hydrophilic carboxylic acid
group. Different fatty acids have different
hydrocarbon tails. Palmitic acid is shown
here. (A) Structural formula, showing the
carboxylic acid head group in its ionized
form, as it exists in water at pH 7. (B) Balland-stick model. (C) Space-filling model
(Movie 2.2).
hydrophilic
carboxylic
acid head
hydrophobic
hydrocarbon tail
_
O
O
C
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
(A)
(B)
(C)
which behaves as an acid (carboxylic acid): in an aqueous solution,
it is ionized (–COO–), extremely hydrophilic, and chemically reactive
(Figure 2–19). Almost all the fatty acid molecules in a cell are covalently
linked to other molecules by their carboxylic acid group (see Panel 2–4,
pp. 72–73). Molecules—such as fatty acids—that possess both hydrophobic and hydrophilic regions are termed amphipathic.
glycerol
glycerol
saturated
fatty acid tails
(A)
unsaturated
fatty acid tails
(B)
Figure 2–20 The properties of fats
depend on the length and saturation of
the fatty acid chains they carry. Fatty acids
are stored in the cytoplasm of many cells
in the form of droplets of triacylglycerol
ECB4 of
E2.19/2.19
molecules made
three fatty acid chains
joined to a glycerol molecule. (A) Saturated
fats are found in meat and dairy products.
(B) Plant oils, such as corn oil, contain
unsaturated fatty acids, which may be
monounsaturated (containing one double
bond) or polyunsaturated (containing
multiple double bonds); this is why plant oils
are liquid at room temperature. Although
fats are essential in the diet, saturated fats
are not: they raise the concentration of
cholesterol in the blood, which tends to
clog the arteries, increasing the risk of heart
attacks and strokes.
ECB4
E2.18/2.18
The hydrocarbon tail of palmitic acid
is saturated:
it has no double bonds
between its carbon atoms and contains the maximum possible number
of hydrogens. Some other fatty acids, such as oleic acid, have unsaturated tails, with one or more double bonds along their length. The double
bonds create kinks in the hydrocarbon tails, interfering with their ability to pack together, and it is the absence or presence of these double
bonds that accounts for the difference between hard (saturated) and soft
(polyunsaturated) margarine. Fatty acid tails are also found in cell membranes, where the tightness of their packing affects the fluidity of the
membrane. The many different fatty acids found in cells differ only in the
length of their hydrocarbon chains and in the number and position of the
carbon–carbon double bonds (see Panel 2–4).
Fatty acids serve as a concentrated food reserve in cells: they can be broken down to produce about six times as much usable energy, weight for
weight, as glucose. Fatty acids are stored in the cytoplasm of many cells
in the form of fat droplets composed of triacylglycerol molecules—compounds made of three fatty acid chains covalently joined to a glycerol
molecule (Figure 2–20, and see Panel 2–4). Triacylglycerols are the animal fats found in meat, butter, and cream, and the plant oils such as
corn oil and olive oil. When a cell needs energy, the fatty acid chains
can be released from triacylglycerols and broken down into two-carbon
units. These two-carbon units are identical to those derived from the
breakdown of glucose, and they enter the same energy-yielding reaction
pathways, as described in Chapter 13.
Fatty acids and their derivatives, including triacylglycerols, are examples
of lipids. Lipids are loosely defined as molecules that are insoluble in
water but soluble in fat and organic solvents such as benzene. They typically contain long hydrocarbon chains, as in the fatty acids, or multiple
linked aromatic rings, as in the steroids (see Panel 2–4).
The most unique function of fatty acids is in the formation of the lipid
bilayer, which is the basis for all cell membranes. These thin sheets,
Small Molecules in Cells
polar
group
hydrophilic
head
water
phosphate
phospholipid
bilayer,
or membrane
fatty acid
two
hydrophobic
fatty acid
tails
fatty acid
glycerol
Figure 2–21 Phospholipids can aggregate
to form cell membranes. Phospholipids
are composed of two hydrophobic fatty
acid tails joined to a hydrophilic head. In an
aqueous environment, the hydrophobic tails
pack together to exclude water, forming a
lipid bilayer, with the hydrophilic heads of
the phospholipid molecules on the outside,
facing the aqueous environment, and the
hydrophobic tails on the inside.
phospholipid molecule
which enclose all cells and surround their internal organelles, are composed largely of phospholipids (Figure 2–21).
Like triacylglycerols, most phospholipids are constructed mainly from fatty
acids and glycerol. In these phospholipids, however, the glycerol is joined
e2.20/2.20
to two fatty acid chains,ECB4
rather
than to three as in triacylglycerols. The
remaining –OH group on the glycerol is linked to a hydrophilic phosphate
group, which in turn is attached to a small hydrophilic compound such
as choline (see Panel 2–4, pp. 72–73). With their two hydrophobic fatty
acid tails and a hydrophilic, phosphate-containing head, phospholipids
are strongly amphipathic. This characteristic amphipathic composition
and shape gives them different physical and chemical properties from
triacylglycerols, which are predominantly hydrophobic. In addition to
phospholipids, cell membranes contain differing amounts of other lipids, including glycolipids, which contain one or more sugars instead of a
phosphate group.
Thanks to their amphipathic nature, phospholipids readily form membranes in water. These lipids will spread over the surface of water to
form a monolayer, with their hydrophobic tails facing the air and their
hydrophilic heads in contact with the water. Two such molecular layers
can readily combine tail-to-tail in water to form the phospholipid sandwich that is the lipid bilayer (see Chapter 11).
Amino Acids Are the Subunits of Proteins
Amino acids are small organic molecules with one defining property:
they all possess a carboxylic acid group and an amino group, both linked
to their α-carbon atom (Figure 2–22). Each amino acid also has a side
chain attached to its α-carbon. The identity of this side chain is what distinguishes one amino acid from another.
amino
group
carboxyl
group
H
H 2N
α-carbon
C
COOH
CH3
H
C
COO
CH3
side chain (R)
nonionized form
(A)
pH 7
+
H 3N
ionized form
(B)
(C)
Figure 2–22 All amino acids have an
amino group, a carboxyl group, and a
side chain (R) attached to their α-carbon
atom. In the cell, where the pH is close to
7, free amino acids exist in their ionized
form; but, when they are incorporated into
a polypeptide chain, the charges on their
amino and carboxyl groups disappear.
(A) The amino acid shown is alanine, one
of the simplest amino acids, which has a
methyl group (CH3) as its side chain.
(B) A ball-and-stick model and (C) a spacefilling model of alanine. In (B) and (C), the
N atom is blue.
55
56
Chapter 2
Chemical Components of Cells
N-terminus of
polypeptide chain
N H
Phe
H C CH2
O C
N H
Ser
H C CH2 OH
O C
N H
Glu
Lys
O
H C CH2 CH2 C _
O
O C
N H
H C
O C
H
CH2 CH2 CH2 CH2 N H+
H
C-terminus of
polypeptide chain
ECB4 E2.22/2.22
Question 2–6
Why do you suppose only l-amino
acids and not a random mixture of
the l- and d-forms of each amino
acid are used to make proteins?
Figure 2–23 Amino acids in a protein are held together by peptide
bonds. The four amino acids shown are linked together by three
peptide bonds, one of which is highlighted in yellow. One of the
amino acids, glutamic acid, is shaded in gray. The amino acid side
chains are shown in red. The two ends of a polypeptide chain are
chemically distinct. One end, the N-terminus, is capped by an amino
group, and the other, the C-terminus, ends in a carboxyl group. The
sequence of amino acids in a protein is abbreviated using either a
three-letter or a one-letter code, and the sequence is always read from
the N-terminus (see Panel 2–5, pp. 74–75). In the example given, the
sequence is Phe-Ser-Glu-Lys (or FSEK).
Cells use amino acids to build proteins—polymers made of amino acids,
which are joined head-to-tail in a long chain that folds up into a threedimensional structure that is unique to each type of protein. The covalent
bond between two adjacent amino acids in a protein chain is called a
peptide bond; the chain of amino acids is also known as a polypeptide.
Peptide bonds are formed by condensation reactions that link one amino
acid to the next. Regardless of the specific amino acids from which it is
made, the polypeptide always has an amino (NH2) group at one end—its
N-terminus—and a carboxyl (COOH) group at its other end—its C-terminus
(Figure 2–23). This difference in the two ends gives a polypeptide a definite directionality—a structural (as opposed to electrical) polarity.
Twenty types of amino acids are commonly found in proteins, each with a
different side chain attached to the α-carbon atom (Panel 2–5, pp. 74–75).
The same 20 amino acids are found in all proteins, whether they hail
from bacteria, plants, or animals. How this precise set of 20 amino acids
came to be chosen is one of the mysteries surrounding the evolution of
life; there is no obvious chemical reason why other amino acids could
not have served just as well. But once the selection had been locked into
place, it could not be changed, as too much chemistry had evolved to
exploit it. Switching the types of amino acids used by cells would require
a living creature to retool its entire metabolism to cope with the new
building blocks.
Like sugars, all amino acids (except glycine) exist as optical isomers in dand l-forms (see Panel 2–5). But only l-forms are ever found in proteins
(although d-amino acids occur as part of bacterial cell walls and in some
antibiotics, and d-serine is used as a signal molecule in the brain). The
origin of this exclusive use of l-amino acids to make proteins is another
evolutionary mystery.
The chemical versatility that the 20 standard amino acids provide is vitally
important to the function of proteins. Five of the 20 amino acids—including lysine and glutamic acid, shown in Figure 2–23—have side chains that
can form ions in solution and can therefore carry a charge. The others
are uncharged. Some amino acids are polar and hydrophilic, and some
are nonpolar and hydrophobic (see Panel 2–5). As we discuss in Chapter
4, the collective properties of the amino acid side chains underlie all the
diverse and sophisticated functions of proteins.
Nucleotides Are the Subunits of DNA and RNA
DNA and RNA are built from subunits called nucleotides. Nucleosides
are made of a nitrogen-containing ring compound linked to a five-carbon
sugar, which can be either ribose or deoxyribose (Panel 2–6, pp. 76–77).
Nucleotides are nucleosides that contain one or more phosphate groups
attached to the sugar, and they come in two main forms: those containing
ribose are known as ribonucleotides, and those containing deoxyribose
are known as deoxyribonucleotides.
Small Molecules in Cells
Figure 2–24 Adenosine triphosphate
(ATP) is a crucially important energy
carrier in cells. (A) Structural formula, in
which the three phosphate groups are
shaded in yellow. (B) Ball-and-stick model
(Movie 2.3). In (B), the P atoms are yellow.
_
phosphoanhydride
_
O
bonds
O
P
O
_
O
O
P
NH2
N
O
H
_
O
C
O
C C
P
CH2 O
N C
N
O
O
C H H C
N C
H
H
H
OH OH
triphosphate
ribose
adenine
adenosine
(A)
(B)
The nitrogen-containing rings of all these molecules are generally referred
to as bases for historical reasons: under acidic conditions, they can each
bind an H+ (proton) and thereby increase the concentration of OH– ions
in aqueous solution. There is a strong family resemblance between the
different nucleotide bases. Cytosine (C), thymine (T), and uracil (U) are
called pyrimidines, because they all derive from a six-membered pyrimidine ring; guanine (G) and adenine (A) are purines, which bear a second,
five-membered ring fused to the six-membered ring. Each nucleotide is
named after the base it contains
(see Panel 2–6, pp. 76–77).
ECB4 e2.23/2.23
Nucleotides can act as short-term carriers of chemical energy. Above
all others, the ribonucleotide adenosine triphosphate, or ATP (Figure
2–24), participates in the transfer of energy in hundreds of metabolic
reactions. ATP is formed through reactions that are driven by the energy
released by the breakdown of foodstuffs. Its three phosphates are linked
in series by two phosphoanhydride bonds (see Panel 2–6). Rupture of these
phosphate bonds releases large amounts of useful energy. The terminal
phosphate group in particular is frequently split off by hydrolysis (Figure
2–25). In many situations, transfer of this phosphate to other molecules
releases energy that drives energy-requiring biosynthetic reactions. Other
nucleotide derivatives serve as carriers for the transfer of other chemical
groups. All of this is described in Chapter 3.
Nucleotides also have a fundamental role in the storage and retrieval of
biological information. They serve as building blocks for the construction
ATP
phosphoanhydride bond
O
_
_
O
_
O
_
ADENINE
O P O P O P O CH2
O
O
O
RIBOSE
input of
energy from
sunlight or
food
O
H+ +
_
H2O
_
O P OH
O
inorganic
phosphate (Pi )
H2O
O
+
_
_
O
_
ADENINE
O P O P O CH2
O
O
RIBOSE
ADP
released energy
available for
intracellular work
and for chemical
synthesis
Figure 2–25 ATP is synthesized from ADP
and inorganic phosphate, and it releases
energy when it is hydrolyzed back to
ADP and inorganic phosphate. The energy
required for ATP synthesis is derived from
either the energy-yielding oxidation of
foodstuffs (in animal cells, fungi, and some
bacteria) or the capture of light (in plant
cells and some bacteria). The hydrolysis
of ATP provides the energy to drive many
processes inside cells. Together, the two
reactions shown form the ATP cycle.
57
58
Chapter 2
Chemical Components of Cells
5′ end
_
O
P
O
O
N
O
5′ CH2 O
NH
N
G
NH2
N
1′
4′
3′
2′
O
_
O
P
O
NH2
O
N
CH2 O
N
N
A
N
O
_
O
P
O
O
H3C
O
CH2 O
NH
T
O
N
O
_
O
Figure 2–26 A short length of one chain of a deoxyribonucleic
acid (DNA) molecule shows the covalent phosphodiester bonds
linking four consecutive nucleotides. Because the bonds link specific
carbon atoms in the sugar ring—known as the 5ʹ and 3ʹ atoms—one
end of a polynucleotide chain, the 5ʹ end, has a free phosphate group
and the other, the 3ʹ end, has a free hydroxyl group. One of the
nucleotides, thymine (T), is shaded in gray, and one phosphodiester
bond is highlighted in yellow. The linear sequence of nucleotides in a
polynucleotide chain is commonly abbreviated by a one-letter code,
and the sequence is always read from the 5ʹ end. In the example
illustrated, the sequence is GATC.
NH2
O
P
N
O
5′ CH2 O
N
1′
4′
3′
O
2′
3′ end
ECB4 e2.25/2.25
C
O
of nucleic acids—long polymers in which nucleotide subunits are linked
by the formation of covalent phosphodiester bonds between the phosphate group attached to the sugar of one nucleotide and a hydroxyl
group on the sugar of the next nucleotide (Figure 2–26). Nucleic acid
chains are synthesized from energy-rich nucleoside triphosphates by
a condensation reaction that releases inorganic pyrophosphate during
phosphodiester bond formation (see Panel 2–6, pp. 76–77).
There are two main types of nucleic acids, which differ in the type of
sugar contained in their sugar–phosphate backbone. Those based on the
sugar ribose are known as ribonucleic acids, or RNA, and contain the
bases A, G, C, and U. Those based on deoxyribose (in which the hydroxyl
at the 2ʹ position of the ribose carbon ring is replaced by a hydrogen) are
known as deoxyribonucleic acids, or DNA, and contain the bases A, G,
C, and T (T is chemically similar to the U in RNA; see Panel 2–6). RNA usually occurs in cells in the form of a single-stranded polynucleotide chain,
but DNA is virtually always in the form of a double-stranded molecule:
the DNA double helix is composed of two polynucleotide chains that run
in opposite directions and are held together by hydrogen bonds between
the bases of the two chains (Panel 2–7, pp. 78–79).
The linear sequence of nucleotides in a DNA or an RNA molecule encodes
genetic information. The two nucleic acids, however, have different roles
in the cell. DNA, with its more stable, hydrogen-bonded helices, acts as
a long-term repository for hereditary information, while single-stranded
RNA is usually a more transient carrier of molecular instructions. The
ability of the bases in different nucleic acid molecules to recognize and
pair with each other by hydrogen-bonding (called base-pairing)—G with
C, and A with either T or U—underlies all of heredity and evolution, as
explained in Chapter 5.
Macromolecules in Cells
On the basis of weight, macromolecules are by far the most abundant of
the organic molecules in a living cell (Figure 2–27). They are the principal
building blocks from which a cell is constructed and also the components
that confer the most distinctive properties on living things. Intermediate
in size and complexity between small organic molecules and organelles,
macromolecules are constructed simply by covalently linking small
organic monomers, or subunits, into long chains, or polymers (Figure
2–28 and How We Know, pp. 60–61). Yet they have many unexpected
properties that could not have been predicted from their simple constituents. For example, it took a long time to determine that the nucleic acids
DNA and RNA store and transmit hereditary information (see How We
Know, pp. 174–176).
Proteins are especially versatile and perform thousands of distinct functions in cells. Many proteins act as enzymes that catalyze the chemical
Macromolecules in Cells
bacterial
cell
30%
chemicals
inorganic ions,
small molecules (4%)
phospholipid (2%)
DNA (1%)
MACROMOLECULE
sugar
polysaccharide
amino
acid
protein
nucleotide
nucleic acid
RNA (6%)
MACROMOLECULES
70%
H2O
SUBUNIT
protein (15%)
polysaccharide (2%)
Figure 2–27 Macromolecules are abundant in cells. The approximate composition
(by mass) of a bacterial cell is shown. The composition of an animal cell is similar.
Figure 2–28 Polysaccharides, proteins,
and nucleic acids are made from
monomeric subunits. Each macromolecule
is a polymer formed from small molecules
(called monomers or subunits) that are
ECB4 e2.27/2.27
linked together by covalent bonds.
e2.26/2.26
reactions that take placeECB4
in cells.
For example, an enzyme in plants, called
ribulose bisphosphate carboxylase, converts CO2 to sugars, thereby creating most of the organic matter used by the rest of the living world. Other
proteins are used to build structural components: tubulin, for example,
self-assembles to make the cell’s long, stiff microtubules (see Figure
1–27B), and histone proteins assemble into spool-like structures that
help wrap up the cell’s DNA in chromosomes. Yet other proteins, such
as myosin, act as molecular motors to produce force and movement. We
examine the molecular basis for many of these wide-ranging functions in
later chapters. Here, we consider some of the general principles of macromolecular chemistry that make all of these activities possible.
Each Macromolecule Contains a Specific Sequence of
Subunits
Although the chemical reactions for adding subunits to each polymer
are different in detail for proteins, nucleic acids, and polysaccharides,
they share important features. Each polymer grows by the addition of a
monomer onto one end of the polymer chain via a condensation reaction, in which a molecule of water is lost with each subunit added (Figure
2–29). In all cases, the reactions are catalyzed by specific enzymes, which
ensure that only the appropriate monomer is incorporated.
The stepwise polymerization of monomers into a long chain is a simple
way to manufacture a large, complex molecule, because the subunits are
added by the same reaction performed over and over again by the same
set of enzymes. In a sense, the process resembles the repetitive operation of a machine in a factory—with some important differences. First,
apart from some of the polysaccharides, most macromolecules are made
from a set of monomers that are slightly different from one another; for
example, proteins are constructed from 20 different amino acids (see
Panel 2–5, pp. 74–75). Second, and most important, the polymer chain is
not assembled at random from these subunits; instead the subunits are
added in a particular order, or sequence.
The biological functions of proteins, nucleic acids, and many polysaccharides are absolutely dependent on the particular sequence of subunits
in the linear chains. By varying the sequence of subunits, the cell can
make an enormous diversity of the polymeric molecules. Thus, for a protein chain 200 amino acids long, there are 20200 possible combinations
(20 × 20 × 20 × 20... multiplied 200 times), while for a DNA molecule
Question 2–7
What is meant by “polarity” of a
polypeptide chain and by “polarity”
of a chemical bond? How do the
meanings differ?
subunit
H
growing polymer
OH + H
H2O
H
Figure 2–29 Macromolecules are formed
by adding subunits to one end. In a
condensation reaction, a molecule of water
is lost with the addition of each monomer to
E2.28/2.28
one endECB4
of the growing
chain. The reverse
reaction—the breakdown of the polymer—
occurs by the addition of water (hydrolysis).
See also Figure 2–18.
59
60
How we Know
what are macromolecules?
The idea that proteins, polysaccharides, and nucleic
acids are large molecules that are constructed from
smaller subunits, linked one after another into long
molecular chains, may seem fairly obvious today. But
this was not always the case. In the early part of the
twentieth century, few scientists believed in the existence of such biological polymers built from repeating
units held together by covalent bonds. The notion that
such “frighteningly large” macromolecules could be
assembled from simple building blocks was considered
“downright shocking” by chemists of the day. Instead,
they thought that proteins and other seemingly large
organic molecules were simply heterogeneous aggregates of small organic molecules held together by weak
“association forces” (Figure 2–30).
The first hint that proteins and other organic polymers
are large molecules came from observing their behavior in solution. At the time, scientists were working with
various proteins and carbohydrates derived from foodstuffs and other organic materials—albumin from egg
whites, casein from milk, collagen from gelatin, and cellulose from wood. Their chemical compositions seemed
simple enough: like other organic molecules, they contained carbon, hydrogen, oxygen, and, in the case of
proteins, nitrogen. But they behaved oddly in solution,
showing, for example, an inability to pass through a fine
filter.
Why these molecules misbehaved in solution was a
puzzle. Were they really giant molecules, composed of
an unusual number of covalently linked atoms? Or were
they more like a colloidal suspension of particles—a
big, sticky hodgepodge of small organic molecules that
associate only loosely?
(A)
(B)
Figure 2–30 What might an organic macromolecule look
like? Chemists in the early part of the twentieth century debated
whether proteins, polysaccharides, and other apparently large
organic molecules were (A) discrete particles made of an
unusually large number of covalently linked atoms or (B) a loose
aggregation of heterogeneous
small organic molecules held
ECB4 e2.29/2.29
together by weak forces.
One way to distinguish between the two possibilities was
to determine the actual size of one of these molecules.
If a protein such as albumin were made of molecules all
identical in size, that would support the existence of true
macromolecules. Conversely, if albumin were instead a
miscellaneous conglomeration of small organic molecules, these should show a whole range of molecular
sizes in solution.
Unfortunately, the techniques available to scientists in
the early 1900s were not ideal for measuring the sizes of
such large molecules. Some chemists estimated a protein’s size by determining how much it would lower a
solution’s freezing point; others measured the osmotic
pressure of protein solutions. These methods were susceptible to experimental error and gave variable results.
Different techniques, for example, suggested that cellulose was anywhere from 6000 to 103,000 daltons in
mass (where 1 dalton is approximately equal to the
mass of a hydrogen atom). Such results helped to fuel
the hypothesis that carbohydrates and proteins were
loose aggregates of small molecules rather than true
macromolecules.
Many scientists simply had trouble believing that
molecules heavier than about 4000 daltons—the largest compound that had been synthesized by organic
chemists—could exist at all. Take hemoglobin, the oxygen-carrying protein in red blood cells. Researchers tried
to estimate its size by breaking it down into its chemical
components. In addition to carbon, hydrogen, nitrogen, and oxygen, hemoglobin contains a small amount
of iron. Working out the percentages, it appeared that
hemoglobin had one atom of iron for every 712 atoms
of carbon—and a minimum weight of 16,700 daltons.
Could a molecule with hundreds of carbon atoms in one
long chain remain intact in a cell and perform specific
functions? Emil Fischer, the organic chemist who determined that the amino acids in proteins are linked by
peptide bonds, thought that a polypeptide chain could
grow no longer than about 30 or 40 amino acids. As
for hemoglobin, with its purported 700 carbon atoms,
the existence of molecular chains of such “truly fantastic lengths” was deemed “very improbable” by leading
chemists.
Definitive resolution of the debate had to await the development of new techniques. Convincing evidence that
proteins are macromolecules came from studies using
the ultracentrifuge—a device that uses centrifugal force
to separate molecules according to their size (see Panel
4–3, pp. 164–165). Theodor Svedberg, who designed the
machine in 1925, performed the first studies. If a protein were really an aggregate of smaller molecules, he
Macromolecules in Cells
reasoned, it would appear as a smear of molecules of
different sizes when sedimented in an ultracentrifuge.
Using hemoglobin as his test protein, Svedberg found
that the centrifuged sample revealed a single, sharp
band with a molecular weight of 68,000 daltons. His
results strongly supported the theory that proteins are
true macromolecules (Figure 2–31).
Additional evidence continued to accumulate throughout the 1930s, as other researchers began to prepare
crystals of pure protein that could be studied by X-ray diffraction. Only molecules with a uniform size and shape
can form highly ordered crystals and diffract X-rays in
such a way that their three-dimensional structure can be
determined, as we discuss in Chapter 4. A heterogeneous suspension could not be studied in this way.
We now take it for granted that large macromolecules
carry out many of the most important activities in living
cells. But chemists once viewed the existence of such
polymers with the same sort of skepticism that a zoologist might show on being told that “In Africa, there are
elephants that are 100 meters long and 20 meters tall.”
It took decades for researchers to master the techniques
required to convince everyone that molecules ten times
larger than anything they had ever encountered were a
cornerstone of biology. As we shall see throughout this
book, such a labored pathway to discovery is not unusual, and progress in science is often driven by
advances in technology.
the sample is loaded as a
narrow band at the top of
the tube
sample
CENTRIFUGATION
61
tube
heterogeneous
aggregates would
sediment to
produce a
diffuse smear
stabilizing
sucrose
gradient
(A)
BOUNDARY SEDIMENTATION
CENTRIFUGATION
BAND SEDIMENTATION
hemoglobin
protein
sediments as a
single band
CENTRIFUGATION
(B)
Figure 2–31 The ultracentrifuge helped to settle the debate about the nature of macromolecules. In the ultracentrifuge,
centrifugal forces exceeding 500,000 times the force of gravity can be used to separate proteins or other large molecules. (A) In a
modern ultracentrifuge, samples are loaded in a thin layer on top of a gradient of sucrose solution formed in a tube. The tube is placed
in a metal rotor that is rotated at high speed. Molecules of different sizes sediment at different rates, and these molecules will therefore
move as distinct bands in the sample tube. If hemoglobin were a loose aggregate of heterogeneous peptides, it would show a broad
smear of sizes after centrifugation (top tube). Instead, it appears as a sharp band with a molecular weight of 68,000 daltons (bottom
tube). Although the ultracentrifuge is now a standard, almost mundane, fixture in most biochemistry laboratories, its construction was
a huge technological challenge. The centrifuge rotor must be capable of spinning centrifuge tubes at high speeds for many hours
at constant temperature and with high stability; otherwise convection occurs in the sedimenting solution and ruins the experiment.
In 1926, Svedberg won the Nobel Prize in Chemistry for his ultracentrifuge design and its application to chemistry. (B) In his actual
experiment, Svedberg filled a special tube in the centrifuge with a homogeneous solution of hemoglobin; by shining light through the
tube, he then carefully monitored the moving boundary
between the sedimenting protein molecules and the clear aqueous solution left
ECB4 e2.30/2.30
behind (so-called boundary sedimentation). The more recently developed method shown in (A) is a form of band sedimentation.
62
Chapter 2
Chemical Components of Cells
10,000 nucleotides long (small by DNA standards), with its four different nucleotides, there are 410,000 different possibilities—an unimaginably
large number. Thus the machinery of polymerization must be subject to a
sensitive control that allows it to specify exactly which subunit should be
added next to the growing polymer end. We discuss the mechanisms that
specify the sequence of subunits in DNA, RNA, and protein molecules in
Chapters 6 and 7.
Noncovalent Bonds Specify the Precise Shape
of a Macromolecule
Question 2–8
In principle, there are many
different, chemically diverse ways in
which small molecules can be linked
to form polymers. For example, the
small molecule ethene (CH2=CH2)
is used commercially to make the
plastic polyethylene (...–CH2–CH2–
CH2–CH2–CH2–...). The individual
subunits of the three major classes
of biological macromolecules,
however, are all linked by similar
reaction mechanisms, i.e., by
condensation reactions that
eliminate water. Can you think of
any benefits that this chemistry
offers and why it might have been
selected in evolution?
Figure 2–32 Most proteins and
many RNA molecules fold into a
particularly stable three-dimensional
shape, or conformation. This shape is
directed mostly by a multitude of weak,
noncovalent intramolecular bonds. If the
folded macromolecules are subjected to
conditions that disrupt noncovalent bonds,
the molecule becomes a flexible chain
that loses both its conformation and its
biological activity.
Most of the single covalent bonds that link together the subunits in a macromolecule allow rotation of the atoms they join; thus the polymer chain
has great flexibility. In principle, this allows a single-chain macromolecule to adopt an almost unlimited number of shapes, or conformations,
as the polymer chain writhes and rotates under the influence of random
thermal energy. However, the shapes of most biological macromolecules
are highly constrained because of weaker, noncovalent bonds that form
between different parts of the molecule. In many cases, these weaker
interactions ensure that the polymer chain preferentially adopts one particular conformation, determined by the linear sequence of monomers
in the chain. Most protein molecules and many of the RNA molecules
found in cells fold tightly into one highly preferred conformation in this
way (Figure 2–32). These unique conformations—shaped by evolution—determine the chemistry and activity of these macromolecules and
dictate their interactions with other biological molecules.
The noncovalent bonds important for the structure and function of macromolecules include two types described earlier: electrostatic attractions
and hydrogen bonds (see Panel 2–7, pp. 78–79). Electrostatic attractions,
although strong on their own, are quite weak in water because the
charged or partially charged (polar) groups involved in the attraction are
shielded by their interactions with water molecules and various inorganic
ions present in the aqueous solution. Electrostatic attractions, however,
are very important in biological systems. An enzyme that binds a positively charged substrate will often use a negatively charged amino acid
side chain to guide its substrate into the proper position.
Earlier, we described the importance of hydrogen bonds in determining
the unique properties of water. They are also very important in the folding of a polypeptide chain and in holding together the two strands of a
double-stranded DNA molecule.
CONDITIONS
THAT DISRUPT
NONCOVALENT
BONDS
a stable folded
conformation
unstructured
polymer chains
Macromolecules in Cells
63
A third type of noncovalent interaction results from van der Waals
attractions, which are a form of electrical attraction caused by fluctuating
electric charges that arise whenever two atoms come within a very short
distance of each other. Although van der Waals attractions are weaker
than hydrogen bonds, in large numbers they play an important role in the
attraction between macromolecules with complementary shapes. All of
these noncovalent bonds are reviewed in Panel 2–7, pp. 78–79.
Another important noncovalent interaction is created by the three-dimensional structure of water, which forces together the hydrophobic portions
of dissolved molecules in order to minimize their disruptive effect on the
hydrogen-bonded network of water molecules (see Panel 2–7 and Panel
2–2, pp. 68–69). This expulsion from the aqueous solution generates what
is sometimes thought of as a fourth kind of noncovalent bond, called a
hydrophobic interaction. Such interactions hold together phospholipid
molecules in cell membranes, for example, and they also play a crucial
part in the folding of protein molecules into a compact globular shape.
Noncovalent Bonds Allow a Macromolecule to Bind Other
Selected Molecules
As we discussed earlier, although noncovalent bonds are individually
weak, they can add up to create a strong attraction between two molecules when these molecules fit together very closely, like a hand in a
glove, so that many noncovalent bonds can occur between them (see
Panel 2–7). This form of molecular interaction provides for great specificity in the binding of a macromolecule to other small and large molecules,
because the multipoint contacts required for strong binding make it possible for a macromolecule to select just one of the many thousands of
different molecules present inside a cell. Moreover, because the strength
of the binding depends on the number of noncovalent bonds that are
formed, associations of almost any strength are possible.
Question 2–9
Why could covalent bonds not be
used in place of noncovalent bonds
to mediate most of the interactions
of macromolecules?
Binding of this type makes it possible for proteins to function as enzymes.
It can also stabilize associations between any macromolecules, as long
as their surfaces match closely (Figure 2–33 and Movie 2.4). Noncovalent
bonds thereby allow macromolecules to be used as building blocks for
the formation of much larger structures. For example, proteins often bind
B
B
A
the surfaces of A and B, and A
and C, are a poor match and
are capable of forming only a few
weak bonds; thermal motion rapidly
breaks them apart
A
A
C
A
A
C
macromolecule A randomly
encounters other
macromolecules (B, C, and D)
D
A
A
D
the surfaces of A and D match
well and therefore can form
enough weak bonds to withstand
thermal jolting; they therefore
stay bound to each other
Figure 2–33 Noncovalent bonds mediate interactions between macromolecules. They can also mediate interactions between a
macromolecule and small molecules (not shown).
64
Chapter 2
Chemical Components of Cells
SUBUNITS
MACROMOLECULES
covalent bonds
amino acids
noncovalent
bonds
MACROMOLECULAR
ASSEMBLY
RNA molecule
nucleotides
globular
protein
30 nm
e.g., ribosome
Figure 2–34 Both covalent bonds and noncovalent bonds are needed to form a macromolecular assembly
such as a ribosome. Covalent bonds allow small organic molecules to join together to form macromolecules, which
can assemble into large macromolecular complexes via noncovalent bonds. Ribosomes are large macromolecular
machines that synthesize proteins inside cells. Each ribosome is composed of about 90 macromolecules (proteins
and RNA molecules), and it is large enough to see in the electron microscope (see Figure 7–31). The subunits,
macromolecules, and the ribosome here are shown roughly to scale.
ECB4 e2.33/2.33
together into multiprotein complexes that function as intricate machines
with multiple moving parts, carrying out such complex tasks as DNA replication and protein synthesis (Figure 2–34). In fact, noncovalent bonds
account for a great deal of the complex chemistry that makes life possible.
Essential Concepts
•
Living cells obey the same chemical and physical laws as nonliving
things. Like all other forms of matter, they are made of atoms, which
are the smallest unit of a chemical element that retain the distinctive
chemical properties of that element.
•
Cells are made up of a limited number of elements, four of which—C,
H, N, O—make up about 96% of a cell’s mass.
•
Each atom has a positively charged nucleus, which is surrounded by
a cloud of negatively charged electrons. The chemical properties of
an atom are determined by the number and arrangement of its electrons: it is most stable when its outer electron shell is completely
filled.
•
A covalent bond forms when a pair of outer-shell electrons is shared
between two adjacent atoms; if two pairs of electrons are shared, a
double bond is formed. Clusters of two or more atoms held together
by covalent bonds are known as molecules.
•
When an electron jumps from one atom to another, two ions of opposite charge are generated; these ions are held together by mutual
attraction forming a noncovalent ionic bond.
•
Living organisms contain a distinctive and restricted set of small
carbon-based (organic) molecules, which are essentially the same
for every living species. The main categories are sugars, fatty acids,
amino acids, and nucleotides.
•
Sugars are a primary source of chemical energy for cells and
can also be joined together to form polysaccharides or shorter
oligosaccharides.
•
Fatty acids are an even richer energy source than sugars, but their
most essential function is to form lipid molecules that assemble into
cell membranes.
•
The vast majority of the dry mass of a cell consists of macromolecules—mainly polysaccharides, proteins, and nucleic acids (DNA
Essential Concepts
and RNA); these macromolecules are formed as polymers of sugars,
amino acids, or nucleotides, respectively.
•
The most diverse and versatile class of macromolecules are proteins,
which are formed from 20 types of amino acids that are covalently
linked by peptide bonds into long polypeptide chains.
•
Nucleotides play a central part in energy-transfer reactions within
cells; they are also joined together to form information-containing
RNA and DNA molecules, each of which is composed of only four
types of nucleotides.
•
Protein, RNA, and DNA molecules are synthesized from subunits by
repetitive condensation reactions, and it is the specific sequence of
subunits that determines their unique functions.
•
Four types of weak noncovalent bonds—hydrogen bonds, electrostatic attractions, van der Waals attractions, and hydrophobic
interactions—enable macromolecules to bind specifically to other
macromolecules or to selected small molecules.
•
The same four types of noncovalent bonds between different regions
of a polypeptide or RNA chain allow these chains to fold into unique
shapes (conformations).
Key terms
acid
amino acid
atom
atomic weight
ATP
Avogadro’s number
base
buffer
chemical bond
chemical group
condensation reaction
conformation
covalent bond
DNA
electron
electrostatic attraction
fatty acid
hydrogen bond
hydrolysis
hydronium ion
hydrophilic
hydrophobic
hydrophobic interactions
inorganic molecule
ion
ionic bond
lipid
lipid bilayer
macromolecule
molecule
molecular weight
monomer
noncovalent bond
nucleotide
organic molecule
pH scale
polar
polymer
protein
proton
RNA
sequence
subunit
sugar
van der Waals attractions
65
66
Panel 2–1
CHEMICAL BONDS AND GROUPS
CARBON SKELETONS
Carbon has a unique role in the cell because of its
ability to form strong covalent bonds with other
carbon atoms. Thus carbon atoms can join to form:
branched trees
rings
chains
C
C
C
C
C
C
C
C
C
C
C
C
C
C–H COMPOUNDS
A covalent bond forms when two atoms come very close
together and share one or more of their outer-shell electrons.
Each atom forms a fixed number of covalent bonds in a
defined spatial arrangement.
Carbon and hydrogen
together make stable
compounds (or groups)
called hydrocarbons. These
are nonpolar, do not form
hydrogen bonds, and are
generally insoluble in water.
SINGLE BONDS: two electrons shared per bond
N
O
Atoms joined by two
or more covalent bonds
cannot rotate freely
around the bond axis.
This restriction has a
major influence on the
three-dimensional shape
of many macromolecules.
DOUBLE BONDS: four electrons shared per bond
C
C
C
also written as
COVALENT BONDS
C
C
C
C
also written as
also written as
C
C
C
C
C
C
N
O
The precise spatial arrangement of covalent bonds influences
the three-dimensional structure and chemistry of molecules.
In this review panel, we see how covalent bonds are used in a
variety of biological molecules.
H
H
C
H
H
H
C
H
H
methane
methyl group
H2C
CH2
H2C
ALTERNATING DOUBLE BONDS
A carbon chain can include double
bonds. If these are on alternate carbon
atoms, the bonding electrons move
within the molecule, stabilizing the
structure by a phenomenon called
resonance.
C
C
C
C
C
C
C
C
C
H
H
C
C
C
C
H
H
CH2
H
C
C
H2C
CH2
H
H
C
C
H2C
H
C
the truth is somewhere between
these two structures
C
H2C
CH2
H
C
CH2
Alternating double bonds in a ring
can generate a very stable structure.
benzene
often written as
H
H
H
H2C
CH2
H3C
part of the hydrocarbon “tail”
of a fatty acid molecule
67
C–O COMPOUNDS
C–N COMPOUNDS
Many biological compounds contain a carbon covalently
bonded to an oxygen. For example,
Amines and amides are two important examples of
compounds containing a carbon linked to a nitrogen.
alcohol
Amines in water combine with an H+ ion to become
positively charged.
H
C
The –OH is called a
hydroxyl group.
OH
H
H
C
H
ketone
O
O
C
C
O
OH
amine
C
C
C
H2O
alcohol
acid
O
C
O
OH
C
amide
H
Nitrogen also occurs in several ring compounds, including
important constituents of nucleic acids: purines and
pyrimidines.
NH2
O
HO
H2O
N
acid
Esters are formed by combining an
acid and an alcohol.
O
C
C
H2N
OH
The –COOH is called a
carboxyl group. In water,
this loses an H_+ ion to
become –COO .
C
C
H
O
C
carboxylic acid
H
N
Amides are formed by combining an acid and an
amine. Unlike amines, amides are uncharged in water.
An example is the peptide bond that joins amino acids
in a protein.
The C O is called a
carbonyl group.
C
esters
C
+
H
C
C
N
O
aldehyde
H
H+
N
C
C
C
N
H
cytosine (a pyrimidine)
H
H
ester
PHOSPHATES
Inorganic phosphate is a stable ion formed from
phosphoric acid, H3PO4. It is also written as Pi .
Phosphate esters can form between a phosphate and a free hydroxyl group.
Phosphate groups are often covalently attached to proteins in this way.
O
HO
O
P
O
O
_
C
OH
HO
_
O
_
O
P
O
_
C
O
_
O
P
also
written as
H2O
C
_
O
O
P
The combination of a phosphate and a carboxyl group, or two or more phosphate groups, gives an acid anhydride. Because
compounds of this type release a large amount of energy when hydrolyzed in the cell, they are often said to contain
a “high-energy” bond.
H2O
O
O
O
HO
C
OH
_
O
P
O
C
_
O
O
O
H2O
O
P
OH
_
O
HO
_
O
P
O
P
O
O
_
H2O
_
O
O
_
_
O
P
O
H2O
high-energy acyl phosphate
bond (carboxylic–phosphoric
acid anhydride) found in
some metabolites
O
O
_
O
P
_
O
high-energy phosphoanhydride
bond found in molecules
such as ATP
also written as
O
C
O
P
also written as
O
P
P
Panel 2–2
68
THE CHEMICAL PROPERTIES OF WATER
HYDROGEN BONDS
Because they are polarized, two
adjacent H2O molecules can form
a noncovalent linkage known as a
hydrogen bond. Hydrogen bonds
have only about 1/20 the strength
of a covalent bond.
hydrogen
bond
0.17 nm
H
H
_
δ
δ+
O
H
O
H
H
Hydrogen bonds are strongest when
the three atoms lie in a straight line.
bond lengths
δ+
δ+
δ
_
O
H
hydrogen
bond
δ+
WATER
H
O
0.10 nm
covalent bond
WATER STRUCTURE
Two atoms connected by a covalent bond may exert different attractions for
the electrons of the bond. In such cases, the bond is polar, with one end
_
slightly negatively charged (δ ) and the other slightly positively charged (δ+).
H
Molecules of water join together transiently
in a hydrogen-bonded lattice.
δ+
electropositive
region
O
δ
δ+
H
_
electronegative
region
δ
_
Although a water molecule has an overall neutral charge (having the same
number of electrons and protons), the electrons are asymmetrically distributed,
making the molecule polar. The oxygen nucleus draws electrons away from
the hydrogen nuclei, leaving the hydrogen nuclei with a small net positive charge.
The excess of electron density on the oxygen atom creates weakly negative
regions at the other two corners of an imaginary tetrahedron. On these pages,
we review the chemical properties of water and see how water influences the
behavior of biological molecules.
The cohesive nature of water is
responsible for many of its unusual
properties, such as high surface tension, high
specific heat, and high heat of vaporization.
HYDROPHILIC MOLECULES
HYDROPHOBIC MOLECULES
Substances that dissolve readily in water are termed hydrophilic. They include
ions and polar molecules that attract water molecules through electrical charge
effects. Water molecules surround each ion or polar molecule and carry it
into solution.
Substances that contain a preponderance
of nonpolar bonds are usually insoluble
in water and are termed hydrophobic.
Water molecules are not attracted to such
hydrophobic molecules and so have little
tendency to surround them and bring them
into solution.
H
H O
H H
H
H
H H
H
O _
δ
H
Oδ
H
H
_
Na+
δ
O
_
_
δ O
H
H
H
H
H δ+
H
O
_
H+
δ
O
H
O
H
H
O
H
δ+ Cl
H
H +
+
δH δ
O
H
O
H
O
O_
δ
H
H
H
N
O
O
H
N
H
O
O
H
C
H
C
H
H
H
Ionic substances such as sodium chloride
dissolve because water molecules are
attracted to the positive (Na+) or negative
_
(Cl ) charge of each ion.
C
H
O
H
H
H
Polar substances such as urea
dissolve because their molecules
form hydrogen bonds with the
surrounding water molecules.
H
H
H
O
H
H
H
H
C
H
O
O
H
H
O
O
H
O
H
H
Hydrocarbons, which contain many
C–H bonds, are especially hydrophobic.
H
69
WATER AS A SOLVENT
Many substances, such as household sugar (sucrose), dissolve in water. That is, their
molecules separate from each other, each becoming surrounded by water molecules.
When a substance dissolves in a
liquid, the mixture is termed a solution.
The dissolved substance (in this case
sugar) is the solute, and the liquid that
does the dissolving (in this case water)
is the solvent. Water is an excellent
solvent for hydrophilic substances
because of its polar bonds.
sugar
dissolves
water
molecule
sugar crystal
sugar molecule
ACIDS
HYDROGEN ION EXCHANGE
Substances that release hydrogen ions (protons) into solution
are called acids.
Positively charged hydrogen ions (H+) can spontaneously
move from one water molecule to another, thereby creating
two ionic species.
+
HCl
H
+
hydrochloric acid
(strong acid)
hydrogen ion
–
Cl
H
chloride ion
H
O
H
H
H
Many of the acids important in the cell are not completely
dissociated, and they are therefore weak acids—for example,
the carboxyl group (–COOH), which dissociates to give a
hydrogen ion in solution.
O
H
C
+
often written as:
H+
H2O
C
hydroxyl ion
+
OH–
hydroxyl
ion
Because the process is rapidly reversible, hydrogen ions are
continually shuttling between water molecules. Pure water
contains equal concentrations of hydronium ions and
hydroxyl ions (both 10–7 M).
(weak acid)
Note that this is a reversible reaction.
BASES
pH
+
H
conc.
moles/liter
10
ACIDIC
The acidity of a
solution is defined
by the concentration
of hydronium ions (H3O+)
it possesses, generally
abbreviated as H+.
For convenience, we
use the pH scale, where
_1
10
10
10
10
10
For pure water
_7
[H+] = 10
moles/liter
ALKALINE
pH = _log10[H+]
pH = 7.0
O
H
hydrogen
ion
O–
OH
H
+
hydronium ion
O
+
+
O H
O
_2
_3
_4
_5
_6
_
pH
1
2
3
4
5
6
10 7
_
10 8
7
8
10
9
10
10
10
10
10
_9
_10
_11
_12
_13
_14
10
11
12
13
14
Substances that reduce the number of hydrogen ions in
solution are called bases. Some bases, such as ammonia,
combine directly with hydrogen ions.
NH3
ammonia
+
H+
NH4+
hydrogen ion
ammonium ion
Other bases, such as sodium hydroxide, reduce the number of
+
–
H ions indirectly, by making OH ions that then combine
+
directly with H ions to make H2O.
+
NaOH
Na
sodium hydroxide
(strong base)
sodium
ion
+
–
OH
hydroxyl
ion
Many bases found in cells are partially associated with H+ ions
and are termed weak bases. This is true of compounds that
contain an amino group (–NH2), which has a weak tendency
to reversibly accept an H+ ion from water, thereby
increasing the concentration of free OH– ions.
–NH2
+
H+
–NH3+
Panel 2–3
an outline of some of the types of sugars
MONOSACCHARIDES
Monosaccharides usually have the general formula (CH2O) n, where n can be 3, 4, 5, or 6, and have two or more hydroxyl groups.
O
They either contain an aldehyde group ( C H ) and are called aldoses, or a ketone group ( C O ) and are called ketoses.
3-carbon (TRIOSES)
5-carbon (PENTOSES)
6-carbon (HEXOSES)
O
H
C
O
H
ALDOSES
C
O
H
C
H
C
OH
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
H
H
glyceraldehyde
ribose
glucose
H
H
H
H
KETOSES
70
H
H
C
OH
C
O
HO
C
H
H
C
OH
C
O
C
OH
H
C
OH
H
C
OH
C
O
H
C
OH
H
C
OH
C
OH
H
C
OH
H
C
OH
H
H
H
dihydroxyacetone
ribulose
fructose
RING FORMATION
ISOMERS
In aqueous solution, the aldehyde or ketone group of a sugar
molecule tends to react with a hydroxyl group of the same
molecule, thereby closing the molecule into a ring.
Many monosaccharides differ only in the spatial arrangement
of atoms—that is, they are isomers. For example, glucose,
galactose, and mannose have the same formula (C6H12O6) but
differ in the arrangement of groups around one or two carbon
atoms.
CH2OH
O
HO
OH
H
H
OH
H
H
O
H
H
2
C
HO C
3
H
H
CH2OH
C
1
4
5
6
OH
H
C
OH
C
OH
H
4
HO
5
O
H
OH
H
1
glucose
H
2
3
H
CH2OH
OH
CH2OH
O
H
OH
H
H
OH
H
HO
OH
6
H
O
1C
H
C
2
OH
H
C
3
OH
H
C
4
OH
CH2OH
O
5
4
H
H
OH
H
1
3
2
H
OH
OH
CH2OH
5
Note that each carbon atom has a number.
ribose
H
OH
glucose
H
OH
galactose
CH2OH
O
H
OH
H
OH
OH
H
HO
H
H
mannose
These small differences make only minor changes in the
chemical properties of the sugars. But the differences are
recognized by enzymes and other proteins and therefore can
have major biological effects.
71
α AND β LINKS
SUGAR DERIVATIVES
The hydroxyl group on the carbon that carries the
aldehyde or ketone can rapidly change from one
position to the other. These two positions are called
α and β.
The hydroxyl groups of
a simple monosaccharide,
such as glucose, can be
replaced by other
groups.
HO
O
O
OH
O
CH2OH
O
OH
H
OH
O
OH
glucosamine
OH
N-acetylglucosamine
glucuronic acid
DISACCHARIDES
+
OH
HO
HO
OH
CH2OH
OH
H2O
CH2OH
O
HOCH2
OH
HO
O
HOCH2
OH
maltose (glucose + glucose)
lactose (galactose + glucose)
sucrose (glucose + fructose)
C
β fructose
O
HO
The reaction forming sucrose is
shown here.
H
O
HO
O
OH
CH2OH
OH
sucrose
OLIGOSACCHARIDES AND POLYSACCHARIDES
Large linear and branched molecules can be made from simple repeating sugar units.
Short chains are called oligosaccharides, and long chains are called polysaccharides.
Glycogen, for example, is a polysaccharide made entirely of glucose units joined together.
glycogen
branch points
CH2OH
COMPLEX OLIGOSACCHARIDES
In many cases, a sugar sequence
is nonrepetitive. Many different
molecules are possible. Such
complex oligosaccharides are
usually linked to proteins or to lipids,
as is this oligosaccharide, which is
part of a cell-surface molecule
that defines a particular blood group.
CH2OH
HO
CH2OH
O
HO
O
O
O
O
NH
C
O
O
CH3
O
OH
O
OH
CH3
HO
OH
O
CH3
CH2OH
α glucose
The carbon that carries the aldehyde
or the ketone can react with any
hydroxyl group on a second sugar
molecule to form a disaccharide.
Three common disaccharides are
OH
NH
OH
As soon as one sugar is linked to another, the α or
β form is frozen.
OH
HO
OH
HO
α hydroxyl
CH2OH
O
NH2
C
β hydroxyl
OH
NH
C
O
CH3
72
Panel 2–4
FATTY ACIDS
All fatty acids have carboxyl
groups at one end and long
hydrocarbon tails at the other.
COOH
COOH
COOH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH2
CH2
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH2
CH2
palmitic
acid
(C16)
CH2
CH3
stearic
acid
(C18)
fatty acids and other lipids
Hundreds of different kinds of fatty acids exist. Some have one or more double bonds in their
hydrocarbon tail and are said to be unsaturated. Fatty acids with no double bonds are saturated.
–O
–O
O
O
C
C
This double bond
is rigid and creates
a kink in the chain.
The rest of the chain
is free to rotate
about the other C–C
bonds.
oleic
acid
space-filling model
carbon skeleton
UNSATURATED
SATURATED
TRIACYLGLYCEROLS
Fatty acids are stored in cells as an energy reserve
(fats and oils) through an ester linkage to
glycerol to form triacylglycerols.
H2C OH
O
H2C
O
CH3
HC
O
oleic
acid
(C18)
H2C
O
CARBOXYL GROUP
C
HC
OH
O
H2C
OH
C
glycerol
O
C
Phospholipids are the major constituents
of cell membranes.
PHOSPHOLIPIDS
If free, the carboxyl group of a
fatty acid will be ionized.
hydrophilic
head
O
O
O
C
stearic
acid
_
O
P
choline
_
O
O
CH2
CH
CH2
But more often it is linked to
other groups to form either esters
O
C
O
C
hydrophobic
fatty acid tails
or amides.
phosphatidylcholine
O
C
N
H
general structure of
a phospholipid
In phospholipids, two of the –OH groups in
glycerol are linked to fatty acids, while the third
–OH group is linked to phosphoric acid. The
phosphate is further linked to one of a variety
of small polar groups, such as choline.
73
LIPID AGGREGATES
POLYISOPRENOIDS
surface film
Fatty acids have a hydrophilic head
and a hydrophobic tail.
Long-chain polymers
of isoprene
O–
micelle
O
In water, they can form either a surface
film or small, spherical micelles.
P
O–
O
Their derivatives can form larger aggregates held together by hydrophobic forces:
Triacylglycerols form large spherical fat
droplets in the cell cytoplasm.
Phospholipids and glycolipids form self-sealing lipid
bilayers, which are the basis for all cell membranes.
200 nm
or more
4 nm
OTHER LIPIDS
STEROIDS
Lipids are defined as water-insoluble
molecules that are soluble in organic
solvents. Two other common types of lipids
are steroids and polyisoprenoids. Both are
made from isoprene units.
CH3
C
CH2
CH
CH2
isoprene
Steroids have a common multiple-ring structure.
OH
HO
cholesterol—found in many cell membranes
O
testosterone—male sex hormone
GLYCOLIPIDS
Like phospholipids, these compounds are composed of a hydrophobic
region, containing two long hydrocarbon tails, and a polar region,
which contains one or more sugars and, unlike phospholipids,
no phosphate.
OH
H
C
C
H
C
H
galactose
H
C
C NH
O
O
CH2
sugar
a simple
glycolipid
dolichol phosphate—used
to carry activated sugars
in the membraneassociated synthesis of
glycoproteins and some
polysaccharides
74
Panel 2–5
the 20 amino acids found in proteins
FAMILIES OF
AMINO ACIDS
BASIC SIDE CHAINS
The common amino acids
are grouped according to
whether their side chains
are
acidic
basic
uncharged polar
nonpolar
lysine
arginine
histidine
(Lys, or K)
(Arg, or R)
(His, or H)
H
O
N
C
C
H
CH2
H
O
N
C
C
H
CH2
CH2
These 20 amino acids
are given both three-letter
and one-letter abbreviations.
CH2
+
NH3
Thus: alanine = Ala = A
This group is
very basic
because its
positive charge
is stabilized by
resonance (see
Panel 2–1).
THE AMINO ACID
NH2
C
R
H
CH2
CH
NH+
The α-carbon atom is asymmetric,
allowing for two mirror-image
(or stereo-) isomers, L and D.
The general formula of an amino acid is
amino
group H2N
C
These nitrogens have a
relatively weak affinity for an
H+ and are only partly positive
at neutral pH.
C
OPTICAL ISOMERS
H
C
HC
NH
2N
N
HN
CH2
+H
O
C
CH2
CH2
H
α-carbon atom
H
carboxyl
COOH group
H
COO–
NH3+
side chain
L
R is commonly one of 20 different side chains.
At pH 7, both the amino and carboxyl groups
are ionized.
H
+
H3N C COO
R
COO–
NH3+
Cα
Cα
R
R
D
Proteins contain exclusively L-amino acids.
PEPTIDE BONDS
The four atoms in each peptide bond (red box) form a rigid
planar unit. There is no rotation around the C–N bond.
In proteins, amino acids are commonly joined together by an
amide linkage, called a peptide bond.
H
H
N
H
C
R
O
C
N
OH
H
H2O
R
H
C
H
O
H
C
N
OH
H
H
O
C
C
R
R
N
C
H
H
O
C
OH
SH
Proteins are long polymers
of amino acids linked by
peptide bonds, and they
are always written with the
N-terminus toward the left.
Peptides are shorter, usually
fewer than 50 amino acids long.
The sequence of this tripeptide
is histidine-cysteine-valine.
amino terminus, or
N-terminus
+H N
3
H
O
C
C
CH2
HC
N
H
C
C
O
H
H
N
C
CH
NH+
carboxyl terminus, or
C-terminus
COO–
CH
CH3
C
HN
CH2
CH3
These two single bonds allow rotation, so that long
chains of amino acids are very flexible.
75
ACIDIC SIDE CHAINS
NONPOLAR SIDE CHAINS
alanine
valine
aspartic acid
glutamic acid
(Ala, or A)
(Val, or V)
(Asp, or D)
(Glu, or E)
H
O
C
H
O
N
C
C
H
CH2
H
O
N
C
N
C
C
H
CH3
H
CH2
O
N
C
C
H
CH
CH3
CH3
CH2
C
O–
O
O–
glutamine
(Asn, or N)
(Gln, or Q)
N
C
C
H
CH2
(Leu, or L)
(Ile, or I)
H
O
N
C
C
H
CH2
NH2
O
N
C
C
H
CH2
H
O
N
C
C
H
CH
CH3
CH3
CH2
CH3
proline
phenylalanine
(Pro, or P)
(Phe, or F)
N
H
O
C
C
CH2
CH2
H
O
N
C
C
H
CH2
CH2
(actually an
imino acid)
CH2
C
H
CH3
asparagine
O
isoleucine
CH
UNCHARGED POLAR SIDE CHAINS
H
leucine
C
O
O
H
C
O
NH2
Although the amide N is not charged at
neutral pH, it is polar.
methionine
tryptophan
(Met, or M)
(Trp, or W)
H
O
N
C
C
H
CH2
H
O
N
C
C
H
CH2
CH2
S
serine
threonine
tyrosine
(Ser, or S)
(Thr, or T)
(Tyr, or Y)
H
O
N
C
C
H
CH2
OH
H
O
N
C
C
H
CH
CH3
H
O
N
C
C
H
CH2
OH
OH
The –OH group is polar.
CH3
N
H
glycine
cysteine
(Gly, or G)
(Cys, or C)
H
O
N
C
C
H
H
H
O
N
C
C
H
CH2
SH
Disulfide bonds can form between two cysteine side chains
in proteins.
S
CH2
CH2 S
76
Panel 2–6
BASES
A SURVEY OF THE NUCLEOTIDES
NH2
O
C
HC
NH2
C
HC
C
HC
U
HC
adenine
NH
uracil
N
H
N
O
4
O
O
H3C
C
C
HC
thymine
NH
T
5
3N
6
2
1
N
N
7
C
N
H
8
9
N
PYRIMIDINE
O
5
1N
4
2
3
N
PURINE
A nucleotide consists of a nitrogen-containing
base, a five-carbon sugar, and one or more
phosphate groups.
O–
–O
P
O
O
P
O–
O–
O
O
P
NH2
O
O–
P
O
O
as in
ADP
CH2
–O
P
CH2
5′
O
O–
O–
P
O
CH2
as in
ATP
O–
The phosphate makes a nucleotide
negatively charged.
Nucleotides
are the
subunits of
the nucleic acids.
SUGARS
3′
2′
OH
PENTOSE
a five-carbon sugar
4’
O
3’
H
H
2’
1’
H
OH
two kinds of
pentoses are used
HOCH2
Each numbered carbon on the sugar of a nucleotide is
followed by a prime mark; therefore, one speaks of the
“5-prime carbon,” etc.
H
SUGAR
C
2′
H
1′
β-D-ribose
used in ribonucleic acid (RNA)
OH
OH
O
β-D-2-deoxyribose
used in deoxyribonucleic acid (DNA)
H
H
H
OH
O
O
OH
O
H
C 5’
N
5′
The base is linked to
the same carbon (C1)
used in sugar–sugar
bonds.
OH
SUGAR
HOCH2
NH2
BASE
3′
1′
C
BASE–SUGAR
LINKAGE
4′
O
4′
O
O
N
G
N
N
PHOSPHATE
O
C
N
H
NH
N-glycosidic
bond
BASE
as in
AMP
CH2
C
HC
O
O
CH
N
C
N
NUCLEOTIDES
The phosphates are normally joined to
the C5 hydroxyl of the ribose or
deoxyribose sugar (designated 5'). Mono-,
di-, and triphosphates are common.
–O
C
N
A
O
6
guanine
PHOSPHATES
P
N
H
cytosine
C
N
H
–O
C
C
HC
The bases are nitrogen-containing ring
compounds, either pyrimidines or purines.
C
N
H
77
NOMENCLATURE
The names can be confusing, but the abbreviations are clear.
BASE
NUCLEOSIDE
ABBR.
adenine
adenosine
A
guanine
guanosine
G
cytosine
cytidine
C
uracil
uridine
U
thymine
thymidine
T
base
Nucleotides are abbreviated by
three capital letters. Some examples
follow:
sugar
BASE + SUGAR = NUCLEOSIDE
AMP = adenosine monophosphate
dAMP = deoxyadenosine monophosphate
UDP = uridine diphosphate
ATP = adenosine triphosphate
base
P
sugar
BASE + SUGAR + PHOSPHATE = NUCLEOTIDE
NUCLEIC ACIDS
NUCLEOTIDES HAVE MANY OTHER FUNCTIONS
Nucleotides are joined together by
phosphodiester bonds between 5’ and
3’ carbon atoms of the sugar ring, via a
phosphate group, to form nucleic acids.
The linear sequence of nucleotides in a
nucleic acid chain is commonly
abbreviated by a one-letter code, such
as AGCTTACA, with the 5’ end of the
chain at the left.
O
–O
P
O
CH2
+
O
N
O
–O
N
O
O
O–
P
O
N
CH2
N
O
O–
O
OH
example: ATP (or ATP )
2
base
OH
NH2
They combine with other groups to form coenzymes.
N
N
CH2
O
sugar
HS
H
H
C
C
H
H2O
H
N
H
O
H
H
C
C
C
H
H
N
H
O
H CH3 H
C
C
C
C
O
O
O
P
O
O–
HO CH3 H
N
P
O
CH2
O–
example: coenzyme A (CoA)
O
5’ end of chain
P
O
5’
CH2
O
base
O
O
3
They are used as small intracellular signaling molecules in the cell.
sugar
3’ O
phosphodiester
–O
bond
P
5’ CH2
NH2
example: cyclic AMP
N
O
O
example: DNA
P
O
P
O–
OH
O–
O
OH
O–
–O
NH2
phosphoanhydride bonds
sugar
O
P
They carry chemical energy in their easily hydrolyzed phosphoanhydride bonds.
base
O–
–O
1
CH2
base
O
O
sugar
3’ OH
3’ end of chain
N
O
O
P
O–
O
OH
N
N
P
O–
N
O
OH
–
O
78
Panel 2–7
the PRINCIPAL TYPES OF WEAK NONCOVALENT BONDS
WEAK NONCOVALENT CHEMICAL BONDS
VAN DER WAALS ATTRACTIONS
Organic molecules can interact with other molecules through
three types of short-range attractive forces known as
noncovalent bonds: van der Waals attractions, electrostatic
attractions, and hydrogen bonds. The repulsion of
hydrophobic groups from water is also important for these
interactions and for the folding of biological macromolecules.
If two atoms are too close together they repel each other
very strongly. For this reason, an atom can often be
treated as a sphere with a fixed radius. The characteristic
“size” for each atom is specified by a unique van der
Waals radius. The contact distance between any two
noncovalently bonded atoms is the sum of their van der
Waals radii.
weak
noncovalent
bond
HYDROGEN BONDS
As already described for water (see Panel 2–2, pp. 68–69),
hydrogen bonds form when a hydrogen atom is
“sandwiched” between two electron-attracting atoms
(usually oxygen or nitrogen).
Hydrogen bonds are strongest when the three atoms are
in a straight line:
H
O
N
H
C
N
O
0.12 nm
radius
0.2 nm
radius
0.15 nm
radius
0.14 nm
radius
At very short distances, any two atoms show a weak
bonding interaction due to their fluctuating electrical
charges. The two atoms will be attracted to each other
in this way until the distance between their nuclei is
approximately equal to the sum of their van der Waals
radii. Although they are individually very weak, such
van der Waals attractions can become important when
two macromolecular surfaces fit very close together,
because many atoms are involved.
Note that when two atoms form a covalent bond, the
centers of the two atoms (the two atomic nuclei) are
much closer together than the sum of the two van der
Waals radii. Thus,
Weak noncovalent bonds have less than 1/20 the strength of
a strong covalent bond. They are strong enough to provide
tight binding only when many of them are formed
simultaneously.
O
H
0.4 nm
two non-bonded
carbon atoms
O
0.15 nm
two carbon
atoms held by
single covalent
bond
0.13 nm
two carbon
atoms held by
double covalent
bond
Examples in macromolecules:
Amino acids in a polypeptide chain can be hydrogen-bonded
together in a folded protein.
R
C
O
H
N
H
H
C
C
H
R
C
C
O
H
N
HYDROGEN BONDS IN WATER
Any two atoms that can form hydrogen bonds to each other
can alternatively form hydrogen bonds to water molecules.
Because of this competition with water molecules, the
hydrogen bonds formed in water between two peptide bonds,
for example, are relatively weak.
R
peptide
bond
O
C
C
N
C
C
H
H
N
C
H
O
C
C
N
C
N
N
H
H
N
H
N
C
C
C
O
C
H
N
H
H
C
O
H
O
2H2O
C
C
C
C
N
H
O
C
N
O
H
H
N
C
H
Two bases, G and C, are hydrogen-bonded in a DNA double helix.
H
O
2H2O
N
H
C
C
79
ELECTROSTATIC ATTRACTIONS
ELECTROSTATIC ATTRACTIONS IN
AQUEOUS SOLUTIONS
Attractive interactions occur both between
fully charged groups (ionic bond) and between
partially charged groups on polar molecules.
δ+
Charged groups are shielded by their
interactions with water molecules.
Electrostatic attractions are therefore
quite weak in water.
δ–
H
O
H
O
The force of attraction between the two partial
charges, δ+ and δ–, falls off rapidly as the
distance between the charges increases.
O
P
H
O
Cl–
Na+
a crystal of
NaCl
O
H
H
H
H
O
O
H
H
H
H
O
In the absence of water, ionic bonds are very strong.
They are responsible for the strength of such
minerals as marble and agate, and for crystal
formation in common table salt, NaCl.
H
H
O
H
H
O
H
O
H
H
O
O
+ H
O + Mg
H
O
H
H
Inorganic ions in solution can also cluster around
charged groups and further weaken these electrostatic
attractions.
Cl
Na
Na
+
+
Cl
H
O
Na
+
H N
+
C
H
Na
O
Cl
+
+
Na
Cl
Cl
Despite being weakened by water and inorganic
ions, electrostatic attractions are very important
in biological systems. For example, an enzyme
that binds a positively charged substrate will
often have a negatively charged amino acid side
chain at the appropriate place.
HYDROPHOBIC INTERACTIONS
substrate
+
H
H
–
C
C
H
H
H
H
C
H
H
H
H
enzyme
H
H
C
Water forces hydrophobic groups together
in order to minimize their disruptive
effects on the water network formed by the H bonds
between water molecules. Hydrophobic groups
held together in this way are sometimes said
to be held together by “hydrophobic
bonds,” even though the attraction is
actually caused by a repulsion from water.
80
Chapter 2
Chemical Components of Cells
Questions
Question 2–10
Question 2–13
Which of the following statements are correct? Explain your
answers.
The elements oxygen and sulfur have similar chemical
properties because they both have six electrons in their
outermost electron shells. Indeed, both elements form
molecules with two hydrogen atoms, water (H2O) and
hydrogen sulfide (H2S). Surprisingly, at room temperature,
water is a liquid, yet H2S is a gas, despite sulfur being much
larger and heavier than oxygen. Explain why this might be
the case.
A. An atomic nucleus contains protons and neutrons.
B. An atom has more electrons than protons.
C. The nucleus is surrounded by a double membrane.
D. All atoms of the same element have the same number
of neutrons.
E. The number of neutrons determines whether the
nucleus of an atom is stable or radioactive.
F. Both fatty acids and polysaccharides can be important
energy stores in the cell.
G. Hydrogen bonds are weak and can be broken by
thermal energy, yet they contribute significantly to the
specificity of interactions between macromolecules.
Question 2–11
To gain a better feeling for atomic dimensions, assume that
the page on which this question is printed is made entirely
of the polysaccharide cellulose, whose molecules are
described by the formula (CnH2nOn), where n can be a quite
large number and is variable from one molecule to another.
The atomic weights of carbon, hydrogen, and oxygen are
12, 1, and 16, respectively, and this page weighs 5 g.
A. How many carbon atoms are there in this page?
B. In cellulose, how many carbon atoms would be stacked
on top of each other to span the thickness of this page (the
size of the page is 21.2 cm × 27.6 cm, and it is 0.07 mm
thick)?
C. Now consider the problem from a different angle.
Assume that the page is composed only of carbon atoms.
A carbon atom has a diameter of 2 × 10–10 m (0.2 nm); how
many carbon atoms of 0.2 nm diameter would it take to
span the thickness of the page?
D. Compare your answers from parts B and C and explain
any differences.
Question 2–12
A. How many electrons can be accommodated in the first,
second, and third electron shells of an atom?
B. How many electrons would atoms of the elements listed
below have to gain or lose to obtain a completely filled
outer shell?
helium
oxygen
carbon
sodium
chlorine
gain __
gain __
gain __
gain __
gain __
lose __
lose __
lose __
lose __
lose __
C. What do the answers tell you about the reactivity of
helium and the bonds that can form between sodium and
chlorine?
Question 2–14
Write the chemical formula for a condensation reaction of
two amino acids to form a peptide bond. Write the formula
for its hydrolysis.
Question 2–15
Which of the following statements are correct? Explain your
answers.
A. Proteins are so remarkably diverse because each is
made from a unique mixture of amino acids that are linked
in random order.
B. Lipid bilayers are macromolecules that are made up
mostly of phospholipid subunits.
C. Nucleic acids contain sugar groups.
D. Many amino acids have hydrophobic side chains.
E. The hydrophobic tails of phospholipid molecules are
repelled from water.
F. DNA contains the four different bases A, G, U, and C.
Question 2–16
A. How many different molecules composed of (a) two,
(b) three, and (c) four amino acids, linked together by
peptide bonds, can be made from the set of 20 naturally
occurring amino acids?
B. Assume you were given a mixture consisting of one
molecule each of all possible sequences of a smallish
protein of molecular weight 4800 daltons. If the average
molecular weight of an amino acid is, say, 120 daltons, how
much would the sample weigh? How big a container would
you need to hold it?
C. What does this calculation tell you about the fraction
of possible proteins that are currently in use by living
organisms (the average molecular weight of proteins is
about 30,000 daltons)?
Question 2–17
This is a biology textbook. Explain why the chemical
principles that are described in this chapter are important
in the context of modern cell biology.
Question 2–18
A. Describe the similarities and differences between van
der Waals attractions and hydrogen bonds.
81
Chapter 2 End-of-Chapter Questions
Question 2–20
B. Which of the two bonds would form (a) between two
hydrogens bound to carbon atoms, (b) between a nitrogen
atom and a hydrogen bound to a carbon atom, and
(c) between a nitrogen atom and a hydrogen bound to
an oxygen atom?
Fatty acids are said to be “amphipathic.” What is meant by
this term, and how does an amphipathic molecule behave
in water? Draw a diagram to illustrate your answer.
Question 2–21
Question 2–19
What are the forces that determine the folding of a
macromolecule into a unique shape?
H
H2N
+
H3N
COOH
C
CH2
Are the formulas in Figure Q2–21 correct or incorrect?
Explain your answer in each case.
H
COO
C
(A)
NH2
R1
CH2
N
C
C
C
O
R2
N
N
(C)
(B)
N
N
SUGAR
(D)
COO
O
O
O
O
P
P
P
O
O
O
O
CH2 O
BASE
CH3
OH
(E)
OH
CH2
OH
(F)
(G)
H
C
H
H
C
H
H
C
H
H
C
H
H
O
H
H
O
H
H
O
H
H
Na
hydrogen bond
H
CH2OH
O
δ
+
O
(I)
δ
–
C
δ
+
HO
O
(H)
O
OH
N
H2N
C
C
OH
OH
OH
(J)
(K)
Figure Q2–21
ECB4 EQ2.22/Q2.22
O
H2O
Cl
Page left intentionally blank
chapter THREE
3
Energy, Catalysis, and
Biosynthesis
One property above all makes living things seem almost miraculously
different from nonliving matter: they create and maintain order in a universe that is tending always toward greater disorder. To accomplish this
remarkable feat, the cells in a living organism must carry out a neverending stream of chemical reactions that produce the molecules the
organism requires to meet its metabolic needs. In some of these reactions, small organic molecules—amino acids, sugars, nucleotides, and
lipids—are taken apart or modified to supply the many other small molecules that the cell requires. In other reactions, these small molecules
are used to construct an enormously diverse range of larger molecules,
including the proteins, nucleic acids, and other macromolecules that
endow living systems with all of their most distinctive properties. Each
cell can be viewed as a tiny chemical factory, performing many millions
of these reactions every second.
To carry out the tremendous number of chemical reactions needed to
sustain it, a living organism requires both a source of atoms in the form
of food molecules and a source of energy. The atoms and the energy must
both come, ultimately, from the nonliving environment. In this chapter,
we discuss why cells require energy, and how they use energy and atoms
from their environment to create the molecular order that makes life
possible.
Most of the chemical reactions that cells perform would normally occur
only at temperatures that are much higher than those inside a cell. Each
reaction therefore requires a major boost in chemical reactivity to enable
it to proceed rapidly within the cell. This boost is provided by specialized
proteins called enzymes, each of which accelerates, or catalyzes, just one
The Use of Energy by Cells
Free Energy and Catalysis
Activated Carriers and
Biosynthesis
84
Chapter 3
Energy, Catalysis, and Biosynthesis
Figure 3–1 A series of enzymecatalyzed reactions forms a metabolic
pathway. Each enzyme catalyzes a
chemical reaction involving a particular
molecule. In this example, a set of
enzymes acting in series converts
molecule A to molecule F, forming a
metabolic pathway.
molecule
molecule
molecule
molecule
molecule
molecule
A
B
C
D
E
F
catalysis by
enzyme 1
catalysis by
enzyme 2
catalysis by
enzyme 3
catalysis by
enzyme 4
catalysis by
enzyme 5
of the many possible kinds of reactions that a particular molecule might
undergo. These enzyme-catalyzed reactions are usually connected in
series, so that the product of one reaction becomes the starting material
for the next (Figure 3–1). The long linear reaction pathways, or metabolic
ECB4linked
e3.01/3.01
pathways, that result are in turn
to one another, forming a complex
web of interconnected reactions.
Rather than being an inconvenience, the necessity for catalysis is a benefit, as it allows the cell to precisely control its metabolism—the sum
total of all the chemical reactions it needs to carry out to survive, grow,
and reproduce. This control is central to the chemistry of life.
Two opposing streams of chemical reactions occur in cells, the catabolic
pathways and the anabolic pathways. The catabolic pathways (catabolism) break down foodstuffs into smaller molecules, thereby generating
both a useful form of energy for the cell and some of the small molecules
that the cell needs as building blocks. The anabolic, or biosynthetic, pathways (anabolism) use the energy harnessed by catabolism to drive the
synthesis of the many molecules that form the cell. Together, these two
sets of reactions constitute the metabolism of the cell (Figure 3–2).
The details regarding the individual reactions that comprise cell metabolism are part of the subject matter of biochemistry, and they need not
concern us here. But the general principles by which cells obtain energy
from their environment and use it to create order are central to cell biology. We begin this chapter with a discussion of why a constant input
of energy is needed to sustain living organisms. We then discuss how
enzymes catalyze the reactions that produce biological order. Finally, we
describe the molecules that carry the energy that makes life possible.
food
molecules
CATABOLIC
PATHWAYS
the many molecules
that form the cell
useful
forms of
energy
+
ANABOLIC
PATHWAYS
lost
heat
the many building blocks
for biosynthesis
Figure 3–2 Catabolic and anabolic
pathways together constitute the cell’s
metabolism. Note that a major portion of
the energy stored in the chemical bonds of
food molecules is dissipated as heat. Thus,
only some of this energy can be converted
to the useful forms of energy needed to
ECB4 e3.02/3.02
drive the synthesis of new molecules.
The Use of Energy by Cells
Nonliving things left to themselves eventually become disordered: buildings crumble and dead organisms decay. Living cells, by contrast, not
only maintain, but actually generate order at every level, from the largescale structure of a butterfly or a flower down to the organization of the
molecules that make up these organisms (Figure 3–3). This property of
life is made possible by elaborate molecular mechanisms that extract
energy from the environment and convert it into the energy stored in
chemical bonds. Biological structures are therefore able to maintain their
form, even though the materials of which they are made are continually being broken down, replaced, and recycled. Your body has the same
basic structure it had 10 years ago, even though you now contain atoms
that, for the most part, were not in your body then.
Biological Order Is Made Possible by the Release of
Heat Energy from Cells
The universal tendency of things to become disordered is expressed in a
fundamental law of physics, the second law of thermodynamics. This law
states that, in the universe or in any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree
of disorder can only increase. The second law of thermodynamics has
such profound implications for living things that it is worth restating in
several ways.
The Use of Energy by Cells
(A)
20 nm
(B)
50 nm
(C)
10 µm
We can express the second law in terms of probability by stating that
systems will change spontaneously toward those arrangements that have
the greatest probability. Consider a box of 100 coins all lying heads up. A
series of events that disturbs the box will tend to move the arrangement
toward a mixture of 50 heads and 50 tails. The reason is simple: there are
a huge number of possible arrangements of the individual
coins that can
ECB4 m2.33/3.03
achieve the 50–50 result, but only one possible arrangement that keeps
them all oriented heads up. Because the 50–50 mixture accommodates a
greater number of possibilities and places fewer constraints on the orientation of each individual coin, we say that it is more “disordered.” For
the same reason, one’s living space will become increasingly disordered
without an intentional effort to keep it organized. Movement toward disorder is a spontaneous process, requiring a periodic input of energy to
reverse it (Figure 3–4).
The measure of a system’s disorder is called the entropy of the system,
and the greater the disorder, the greater the entropy. Thus another way
to express the second law of thermodynamics is to say that systems
will change spontaneously toward arrangements with greater entropy.
Living cells—by surviving, growing, and forming complex communities
and even whole organisms—generate order and thus might appear to
defy the second law of thermodynamics. This is not the case, however,
(D)
0.5 mm
(E)
20 mm
Figure 3–3 Biological structures are
highly ordered. Well-defined, ornate, and
beautiful spatial patterns can be found
at every level of organization in living
organisms. In order of increasing size:
(A) protein molecules in the coat of a virus
(a parasite that, although not technically
alive, contains the same types of molecules
as those found in living cells); (B) the regular
array of microtubules seen in a cross section
of a sperm tail; (C) surface contours of a
pollen grain (a single cell); (D) cross section
of a fern stem, showing the patterned
arrangement of cells; and (E) flower with a
spiral array of petals, each made of millions
of cells. (A, courtesy of Robert Grant,
Stéphane Crainic, and James M. Hogle;
B, courtesy of Lewis Tilney; C, courtesy of
Colin MacFarlane and Chris Jeffree;
D, courtesy of Jim Haseloff.)
ORGANIZED EFFORT REQUIRING ENERGY INPUT
“SPONTANEOUS“ REACTION
as time elapses
Figure 3–4 The spontaneous tendency
toward disorder is an everyday
experience. Reversing this natural tendency
toward disorder requires an intentional
effort and an input of energy. In fact, from
the second law of thermodynamics, we
can be certain that the human intervention
required will release enough heat to the
environment to more than compensate for
the reestablishment of order in this room.
85
86
Chapter 3
Energy, Catalysis, and Biosynthesis
Figure 3–5 Living cells do not defy the
second law of thermodynamics. In the
diagram on the left, the molecules of both
the cell and the rest of the universe (the
environment) are depicted in a relatively
disordered state. In the diagram on the
right, the cell has taken in energy from food
molecules and released heat by carrying out
a reaction that orders the molecules that the
cell contains. Because the heat increases
the disorder in the environment around the
cell—as depicted by the longer, jagged red
arrows, which represent increased thermal
motion, and the distorted molecules,
which indicate enhanced molecular
vibration and rotation—the second law of
thermodynamics is satisfied, even as the cell
grows and constructs larger molecules.
sea of matter
cell
HEAT
increased disorder
increased order
because a cell is not an isolated system. Rather, it takes in energy from
ECB4 e3.05/3.05
its environment—in the form of
food, inorganic molecules, or photons of
light from the sun—and it then uses this energy to generate order within
itself, forging new chemical bonds and building large macromolecules.
In the course of performing the chemical reactions that generate order,
some energy is lost in the form of heat. Heat is energy in its most disordered form—the random jostling of molecules (analogous to the random
jostling of the coins in the box). Because the cell is not an isolated system, the heat energy that its reactions generate is quickly dispersed into
the cell’s surroundings. There, the heat increases the intensity of the thermal motions of nearby molecules, thereby increasing the entropy of the
environment (Figure 3–5).
The amount of heat released by a cell must be great enough that the
increased order generated inside the cell is more than compensated for
by the increased disorder generated in the environment. Only in this case
is the second law of thermodynamics satisfied, because the total entropy
of the system—that of the cell plus its environment—increases as a result
of the chemical reactions inside the cell.
Cells Can Convert Energy from One Form to Another
According to the first law of thermodynamics, energy cannot be created or
destroyed—but it can be converted from one form to another (Figure 3–6).
Cells take advantage of this law of thermodynamics, for example, when
they convert the energy from sunlight into the energy in the chemical
bonds of sugars and other small organic molecules during photosynthesis. Although chemical reactions that power such energy conversions can
change how much energy is present in one form or another, the first law
tells us that the total amount of energy in the universe must always be
the same.
When an animal cell breaks down foodstuffs, some of the energy in
the chemical bonds in the food molecules (chemical-bond energy) is
converted into the thermal motion of molecules (heat energy). This conversion of chemical energy into heat energy causes the universe as a
whole to become more disordered—as required by the second law of thermodynamics. But the cell cannot derive any benefit from the heat energy
it produces unless the heat-generating reactions are directly linked to
processes that maintain molecular order inside the cell. It is the tight
coupling of heat production to an increase in order that distinguishes the
metabolism of a cell from the wasteful burning of fuel in a fire. Later in
this chapter, we illustrate how this coupling occurs. For the moment, it is
The Use of Energy by Cells
falling brick has
kinetic energy
raised brick
has potential
energy due
to pull of
gravity
A
heat is released
when brick hits
the floor
potential energy due to position
kinetic energy
heat energy
+
two hydrogen
gas molecules
B
oxygen gas
molecule
rapid vibrations and
rotations of two newly
formed water molecules
rapid molecular
motions in H2O
(kinetic energy)
chemical-bond energy in H2 and O2
battery
–
heat dispersed to
surroundings
heat energy
fan
motor
Figure 3–6 Different forms of energy
are interconvertible, but the total amount
of energy must be conserved. In (A), we
can use the height and weight of the brick
to predict exactly how much heat will be
released when it hits the floor. In (B), the
large amount of chemical-bond energy
released when water (H2O) is formed from
H2 and O2 is initially converted to very
rapid thermal motions in the two new H2O
molecules; however, collisions with other
H2O molecules almost instantaneously
spread this kinetic energy evenly throughout
the surroundings (heat transfer), making
the new H2O molecules indistinguishable
from all the rest. (C) Cells can convert
chemical-bond energy into kinetic energy
to drive, for example, molecular motor
proteins; however, this occurs without the
intermediate conversion to electrical energy
that a man-made appliance such as this fan
requires. (D) Some cells can also harvest
the energy from sunlight to form chemical
bonds via photosynthesis.
–
+
+
wires
fan
C
chemical-bond energy
sunlight
D
electromagnetic (light) energy
electrical energy
chlorophyll
molecule
chlorophyll molecule
in excited state
high-energy electrons
kinetic energy
photosynthesis
chemical-bond energy
sufficient to recognize that—by directly linking the “burning” of food molECB4 e3.06/3.06
ecules to the generation of biological order—cells are able to create and
maintain an island of order in a universe tending toward chaos.
Photosynthetic Organisms Use Sunlight to Synthesize
Organic Molecules
All animals live on energy stored in the chemical bonds of organic molecules, which they take in as food. These food molecules also provide the
atoms that animals need to construct new living matter. Some animals
obtain their food by eating other animals, others by eating plants. Plants,
by contrast, obtain their energy directly from sunlight. Thus, the energy
animals obtain by eating plants—or by eating animals that have eaten
plants—ultimately comes from the sun (Figure 3–7).
Solar energy enters the living world through photosynthesis, a process
that converts the electromagnetic energy in sunlight into chemical-bond
energy in cells. Photosynthetic organisms—including plants, algae, and
Figure 3–7 With few exceptions, the
radiant energy of sunlight sustains
all life. Trapped by plants and some
microorganisms through photosynthesis,
light from the sun is the ultimate source of
all energy for humans and other animals.
(Wheat Field Behind Saint-Paul Hospital
with a Reaper by Vincent van Gogh.
Courtesy of Museum Folkwang, Essen.)
ECB4 e3.07/3.07
87
88
Chapter 3
Energy, Catalysis, and Biosynthesis
PHOTOSYNTHESIS
SUN
activated
carriers
of energy
capture of
light energy
H2O
O2
STAGE 1
Figure 3–8 Photosynthesis takes place
in two stages. The activated carriers
generated in the first stage are two
molecules that we will discuss shortly:
ATP and NADPH.
manufacture
of sugars
H2O + CO2
SUGAR
STAGE 2
some bacteria—use the energy they derive from sunlight to synthesize
small chemical building blocks such as sugars, amino acids, nucleotides,
and fatty acids. These small molecules in turn are converted into the
macromolecules—the proteins, nucleic acids, polysaccharides, and lipECB4 e3.08/3.08
ids—that form
the plant.
We describe the elegant mechanisms that underlie photosynthesis in
detail in Chapter 14. Generally speaking, the reactions of photosynthesis take place in two stages. In the first stage, energy from sunlight is
captured and transiently stored as chemical-bond energy in specialized
molecules called activated carriers, which we discuss in more detail later
in the chapter. All of the oxygen (O2) in the air we breathe is generated by
the splitting of water molecules during this first stage of photosynthesis.
Question 3–1
Consider the equation
light energy + CO2 + H2O →
sugars + O2 + heat energy
Would you expect this reaction to
occur in a single step? Why must
heat be generated in the reaction?
Explain your answers.
In the second stage, the activated carriers are used to help drive a carbonfixation process, in which sugars are manufactured from carbon dioxide
gas (CO2). In this way, photosynthesis generates an essential source of
stored chemical-bond energy and other organic materials—for the plant
itself and for any animals that eat it. The two stages of photosynthesis are
summarized in Figure 3–8.
Cells Obtain Energy by the Oxidation of Organic
Molecules
All animal and plant cells require the chemical energy stored in the
chemical bonds of organic molecules—either the sugars that a plant has
produced by photosynthesis as food for itself or the mixture of large and
small molecules that an animal has eaten. To use this energy to live,
grow, and reproduce, organisms must extract it in a usable form. In both
plants and animals, energy is extracted from food molecules by a process
of gradual oxidation, or controlled burning.
Earth’s atmosphere is about 21% oxygen. In the presence of oxygen, the
most energetically stable form of carbon is CO2 and that of hydrogen is
H2O. A cell is therefore able to obtain energy from sugars or other organic
molecules by allowing the carbon and hydrogen atoms in these molecules to combine with oxygen—that is, become oxidized—to produce CO2
and H2O, respectively—a process known as cellular respiration.
Photosynthesis and cellular respiration are complementary processes
(Figure 3–9). This means that the transactions between plants and animals are not all one way. Plants, animals, and microorganisms have
existed together on this planet for so long that they have become an
essential part of each other’s environments. The oxygen released by
photosynthesis is consumed by nearly all organisms for the oxidative
breakdown of organic molecules. And some of the CO2 molecules that
today are incorporated into organic molecules by photosynthesis in a
green leaf were released yesterday into the atmosphere by the respiration of an animal, a fungus, or the plant itself, or by the burning of
The Use of Energy by Cells
PHOTOSYNTHESIS
CO2 + H2O
O2
H2O
CELLULAR RESPIRATION
O2 + SUGARS
SUGARS + O2
CO2
CO2
PLANTS
ALGAE
SOME BACTERIA
SUGARS AND
OTHER ORGANIC
MOLECULES
H2O + CO2
O2
MOST
LIVING
ORGANISMS
H2O
USEFUL
CHEMICALBOND
ENERGY
ENERGY
OF
SUNLIGHT
fossil fuels. Carbon utilization therefore forms a huge cycle that involves
the biosphere (all of the living organisms on Earth) as a whole, crossing
boundaries between individual organisms (Figure 3–10).
Oxidation and Reduction Involve Electron Transfers
ECB4 e3.09/3.09
The cell does not oxidize organic molecules in one step, as occurs when
organic material is burned in a fire. Through the use of enzyme catalysts,
metabolism directs the molecules through a large number of reactions,
few of which actually involve the direct addition of oxygen. Thus, before
we consider some of these reactions, we should explain what is meant
by oxidation.
Figure 3–9 Photosynthesis and cellular
respiration are complementary processes
in the living world. The left side of the
diagram shows how photosynthesis—
carried out by plants and photosynthetic
microorganisms—uses the energy of
sunlight to produce sugars and other
organic molecules from the carbon
atoms in CO2 in the atmosphere. In
turn, these molecules serve as food for
other organisms. The right side of the
diagram shows how cellular respiration
in most organisms—including plants and
photosynthetic microorganisms—uses O2
to oxidize food molecules, releasing the
same carbon atoms in the form of CO2
back to the atmosphere. In the process,
the organisms obtain the useful chemicalbond energy that they need to survive.
The first cells on Earth are thought to have
been capable of neither photosynthesis nor
cellular respiration (discussed in Chapter
14). However, photosynthesis must have
preceded respiration on the Earth, because
there is strong evidence that billions of
years of photosynthesis were required to
release enough O2 to create an atmosphere
that could support respiration.
The term oxidation literally means the addition of oxygen atoms to a molecule. More generally, though, oxidation is said to occur in any reaction
in which electrons are transferred from one atom to another. Oxidation,
in this sense, refers to the removal of electrons from an atom. The converse reaction, called reduction, involves the addition of electrons to an
atom. Thus, Fe2+ is oxidized when it loses an electron to become Fe3+,
whereas a chlorine atom is reduced when it gains an electron to become
Cl–. Because the number of electrons is conserved in a chemical reaction (there is no net loss or gain), oxidation and reduction always occur
simultaneously: that is, if one molecule gains an electron in a reaction
(reduction), a second molecule must lose the electron (oxidation). When
a sugar molecule is oxidized to CO2 and H2O, for example, the O2 molecules involved in forming H2O gain electrons and thus are said to have
been reduced.
The terms oxidation and reduction apply even when there is only a partial
shift of electrons between atoms linked by a covalent bond. When a carbon atom becomes covalently bonded to an atom with a strong affinity
for electrons—oxygen, chlorine, or sulfur, for example—it gives up more
CO2 IN ATMOSPHERE AND WATER
CELLULAR RESPIRATION
PHOTOSYNTHESIS
PLANTS, ALGAE,
BACTERIA
ANIMALS
FOOD
CHAIN
HUMUS AND DISSOLVED
ORGANIC MATTER
SEDIMENTS AND
FOSSIL FUELS
Figure 3–10 Carbon atoms cycle
continuously through the biosphere.
Individual carbon atoms are incorporated
into organic molecules of the living world by
the photosynthetic activity of plants, algae,
and bacteria. They then pass to animals
and microorganisms—as well as into
organic material in soil and oceans—and
are ultimately restored to the atmosphere
in the form of CO2 when organic molecules
are oxidized by cells during respiration or
burned by humans as fossil fuels.
89
Chapter 3
(A)
_
_
e
+
ATOM 1
Energy, Catalysis, and Biosynthesis
+
_
e
_
e
e
+
FORMATION OF
A POLAR
COVALENT
BOND
_
e
ATOM 2
partial
positive
charge (δ+)
oxidized
(B)
_
e
+ _
e
H
+
MOLECULE
H methane
partial
negative
charge (δ–)
reduced
O
H
H
R
H methanol
I
D
Figure 3–11 Oxidation and reduction involve a shift in the balance of electrons.
(A) When two atoms form a polar covalent bond (as discussed in Chapter 2, p. 44), the
atom that ends up with a greater share of electrons (represented by the blue clouds)
is said to be reduced, while the other atom, with a lesser share of electrons, is said to
be oxidized. The reduced atom has acquired a partial negative charge (δ–); conversely,
the oxidized atom has acquired a partial positive charge (δ+), as the positive charge
on the atomic nucleus now exceeds the total charge of the electrons surrounding it.
(B) A simple reduced carbon compound, such as methane, can be oxidized in a stepwise
fashion by the successive replacement of its covalently bonded hydrogen atoms with
oxygen atoms. With each step, electrons are shifted away from the carbon, and the
carbon atom becomes progressively more oxidized. Moving in the opposite direction,
carbon dioxide becomes progressively more reduced as its oxygen atoms are replaced
by hydrogens to yield methane.
C
X
H
T
N
OH
formaldehyde
H
C
I
O
C
H
A
O
E
D
U
C
T
I
H
H
formic acid
C
O
C
O
O
N
HO
O
90
carbon dioxide
than its equal share of electrons and forms a polar covalent bond. The
positive charge of the carbon nucleus now slightly exceeds the negative
charge of its electrons, so that the carbon atom acquires a partial positive
charge (δ+) and is said to be oxidized. Conversely, the carbon atom in a
C–H bond has somewhat more than its share of electrons; it acquires a
ECB4 e3.11/3.11
partial negative charge (δ–), and so is said to be reduced (Figure 3–11A).
When a molecule in a cell picks up an electron (e–), it often picks up a
proton (H+) at the same time (protons being freely available in water).
The net effect in this case is to add a hydrogen atom to the molecule:
A + e– + H+ → AH
Even though a proton plus an electron is involved (instead of just an
electron), such hydrogenation reactions are reductions, and the reverse,
dehydrogenation, reactions are oxidations. An easy way to tell whether an
organic molecule is being oxidized or reduced is to count its C–H bonds:
reduction occurs when the number of C–H bonds increases, whereas oxidation occurs when the number of C–H bonds decreases (Figure 3–11B).
As we will see later in this chapter—and again in Chapter 13—cells use
enzymes to catalyze the oxidation of organic molecules in small steps,
through a sequence of reactions that allows energy to be harvested in
useful forms.
Free Energy and Catalysis
Enzymes, like cells, obey the second law of thermodynamics. Although
they can speed up energetically favorable reactions—those that produce
disorder in the universe—enzymes cannot by themselves force energetically unfavorable reactions to occur. Cells, however, must do just that
in order to grow and divide—or just to survive. They must build highly
ordered and energy-rich molecules from small and simple ones—a process that requires an input of energy.
To understand how enzymes promote catalysis—the acceleration of
the specific chemical reactions needed to sustain life—we first need to
examine the energetics involved. In this section, we consider how the
free energy of molecules contributes to their chemistry, and we see how
Free Energy and Catalysis
free-energy changes—which reflect how much total disorder is generated
in the universe by a reaction—influence whether and how the reaction
will proceed. We then discuss how enzymes lower the activation energy
needed to initiate reactions in the cell. And we describe how enzymes
can exploit differences in the free-energy changes of different reactions
to drive the energetically unfavorable reactions that produce biological
order. Such enzyme-assisted catalysis is crucial for cells: without it, life
could not exist.
Chemical Reactions Proceed in the Direction that Causes
a Loss of Free Energy
Paper burns readily, releasing into the atmosphere water and carbon
dioxide as gases, while simultaneously releasing energy as heat:
paper + O2 → smoke + ashes + heat + CO2 + H2O
This reaction occurs in only one direction: smoke and ashes never spontaneously gather carbon dioxide and water from the heated atmosphere
and reconstitute themselves into paper. When paper burns, much of its
chemical energy is dissipated as heat: it is not lost from the universe,
since energy can never be created or destroyed; instead, it is irretrievably
dispersed in the chaotic random thermal motions of molecules. At the
same time, the atoms and molecules of the paper become dispersed and
disordered. In the language of thermodynamics, there has been a release
of free energy—that is, energy that can be harnessed to do work or drive
chemical reactions. This release reflects a loss of orderliness in the way
the energy and molecules had been stored in the paper. We will discuss
free energy in more detail shortly, but the general principle can be summarized as follows: chemical reactions proceed only in the direction that
leads to a loss of free energy. In other words, the spontaneous direction
for any reaction is the direction that goes “downhill.” A “downhill” reaction in this sense is said to be energetically favorable.
Question 3–2
In which of the following reactions
does the red atom undergo an
oxidation?
A. Na → Na+ (Na atom → Na+ ion)
B. Cl → Cl–
(Cl atom → Cl– ion)
C. CH3CH2OH → CH3CHO
(ethanol → acetaldehyde)
D. CH3CHO → CH3COO–
(acetaldehyde → acetic acid)
E. CH2=CH2 → CH3CH3
(ethene → ethane)
Enzymes Reduce the Energy Needed to Initiate
Spontaneous Reactions
a
activation
energy for
reaction
Y X
total energy
total energy
Although the most energetically favorable form of carbon under ordinary conditions is CO2, and that of hydrogen is H2O, a living organism
will not disappear in a puff of smoke, and the book in your hands will
not burst spontaneously into flames. This is because the molecules in
both the living organism and the book are in a relatively stable state, and
they cannot be changed to lower-energy states without an initial input
of energy. In other words, a molecule requires a boost over an energy
barrier before it can undergo a chemical reaction that moves it to a lowerenergy (more stable) state (Figure 3–12A). This boost is known as the
Y
b
reactant
Y
d
enzyme lowers
activation
energy for
catalyzed
reaction
Y X
b
reactant
X
X
product
(A)
uncatalyzed
reaction pathway
c
product
(B)
enzyme-catalyzed
reaction pathway
c
Figure 3–12 Even energetically favorable
reactions require activation energy to get
them started. (A) Compound Y (a reactant)
is in a relatively stable state; thus energy
is required to convert it to compound X
(a product), even though X is at a lower
overall energy level than Y. This conversion
will not take place, therefore, unless
compound Y can acquire enough activation
energy (energy a minus energy b) from its
surroundings to undergo the reaction that
converts it into compound X. This energy
may be provided by means of an unusually
energetic collision with other molecules. For
the reverse reaction, X → Y, the activation
energy required will be much larger (energy
a minus energy c); this reaction will therefore
occur much more rarely. Activation energies
are always positive. The total energy change
for the energetically favorable reaction
Y → X, is energy c minus energy b, a
negative number, which corresponds to
a loss of free energy. (B) Energy barriers
for specific reactions can be lowered by
catalysts, as indicated by the line marked d.
Enzymes are particularly effective catalysts
because they greatly reduce the activation
energy for the reactions they catalyze.
91
Chapter 3
Energy, Catalysis, and Biosynthesis
Figure 3–13 Lowering the activation
energy greatly increases the probability
that a reaction will occur. At any given
instant, a population of identical substrate
molecules will have a range of energies,
distributed as shown on the graph. The
varying energies come from collisions with
surrounding molecules, which make the
substrate molecules jiggle, vibrate, and
spin. For a molecule to undergo a chemical
reaction, the energy of the molecule must
exceed the activation energy barrier for that
reaction (dashed lines); for most biological
reactions, this almost never happens
without enzyme catalysis. Even with enzyme
catalysis, only a small fraction of substrate
molecules reach an energy state that is high
enough for them to undergo a reaction (red
shaded area).
energy required
to undergo
the enzyme-catalyzed
chemical reaction
number of molecules
energy needed
to undergo an
uncatalyzed
chemical reaction
energy per molecule
molecules with
average energy
activation energy. In the case of a burning book, the activation energy is
provided by the heat of a lighted match. But cells can’t raise their temperature to drive biological reactions. Inside cells, the push over the energy
ECB4 e3.13/3.13
barrier is aided by specialized proteins called enzymes.
Figure 3–14 Enzymes catalyze reactions
by lowering the activation energy barrier.
(A) The dam represents the activation
energy, which is lowered by enzyme
catalysis. Each green ball represents
a potential substrate molecule that is
bouncing up and down in energy level
owing to constant encounters with waves,
an analogy for the thermal bombardment of
substrate molecules by surrounding water
molecules. When the barrier—the activation
energy—is lowered significantly, the balls
(substrate molecules) with sufficient energy
can roll downhill, an energetically favorable
movement. (B) The four walls of the box
represent the activation energy barriers
for four different chemical reactions that
are all energetically favorable because the
products are at lower energy levels than
the substrates. In the left-hand box, none
of these reactions occurs because even
the largest waves are not large enough
to surmount any of the energy barriers.
In the right-hand box, enzyme catalysis
lowers the activation energy for reaction
number 1 only; now the jostling of the waves
allows the substrate molecule to pass over
this energy barrier, allowing reaction 1 to
proceed (Movie 3.1). (C) A branching river
with a set of barrier dams (yellow boxes)
serves to illustrate how a series of enzymecatalyzed reactions determines the exact
reaction pathway followed by each molecule
inside the cell by controlling specifically
which reaction will be allowed at each
junction.
Each enzyme binds tightly to one or two molecules, called substrates,
and holds them in a way that greatly reduces the activation energy needed
to facilitate a specific chemical interaction between them (Figure 3–12B).
A substance that can lower the activation energy of a reaction is termed
a catalyst; catalysts increase the rate of chemical reactions because they
allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates over the energy barrier, as illustrated
in Figure 3–13 and Figure 3–14A. Enzymes are among the most effective
catalysts known. They can speed up reactions by a factor of as much
as 1014 (that is, trillions of times faster than the same reactions would
proceed without an enzyme catalyst). Enzymes therefore allow reactions
that would not otherwise occur to proceed rapidly at the normal temperature inside cells.
dry
river
bed
lake with
waves
uncatalyzed reaction—waves not large
enough to surmount barrier
flowing
stream
catalyzed reaction—waves often surmount barrier
(A)
2
3
1
4
2
3
energy
92
uncatalyzed
(B)
1
4
enzyme catalysis
of reaction 1
(C)
Free Energy and Catalysis
enzyme
enzyme
active site
molecule A
(substrate)
CATALYSIS
enzyme–
substrate
complex
enzyme–
product
complex
molecule B
(product)
Figure 3–15 Enzymes convert substrates
to products while remaining unchanged
themselves. Each enzyme has an active site
to which one or two substrate molecules
bind, forming an enzyme–substrate
complex. A reaction occurs at the active
site, generating an enzyme–product
complex. The product is then released,
allowing the enzyme to bind additional
substrate molecules and repeat the
reaction. An enzyme thus serves as a
catalyst, and it usually forms or breaks
a single covalent bond in a substrate
molecule.
Unlike the effects of temperature, enzymes are highly selective. Each
ECB4 e3.15/3.15
enzyme usually speeds up only
one particular reaction out of the several possible reactions that its substrate molecules could undergo. In this
way, enzymes direct each of the many different molecules in a cell along
specific reaction pathways (Figure 3–14B and C), thereby producing the
compounds that the cell actually needs.
Like all catalysts, enzyme molecules themselves remain unchanged after
participating in a reaction and therefore can function over and over again
(Figure 3–15). In Chapter 4, we will discuss further how enzymes work,
after we have looked in detail at the molecular structure of proteins.
The Free-Energy Change for a Reaction Determines
Whether It Can Occur
According to the second law of thermodynamics, a chemical reaction
can proceed only if it results in a net (overall) increase in the disorder of
the universe (see Figure 3–5). Disorder increases when useful energy that
could be harnessed to do work is dissipated as heat. The useful energy in
a system is known as its free energy, or G. And because chemical reactions involve a transition from one molecular state to another, the term
that is of most interest to chemists and cell biologists is the free-energy
change, denoted ΔG (“Delta G”).
Let’s consider a collection of molecules. ΔG measures the amount of disorder created in the universe when a reaction involving these molecules
takes place. Energetically favorable reactions, by definition, are those that
create disorder by decreasing the free energy of the system to which they
belong; in other words, they have a negative ΔG (Figure 3–16).
A reaction can occur spontaneously only if ΔG is negative. On a macroscopic scale, an energetically favorable reaction with a negative ΔG is the
relaxation of a compressed spring into an expanded state, releasing its
stored elastic energy as heat to its surroundings. On a microscopic scale,
an energetically favorable reaction with a negative ΔG occurs when salt
(NaCl) dissolves in water. Note that, just because a reaction can occur
spontaneously, does not mean it will occur quickly. The decay of diamonds into graphite is a spontaneous process—but it takes millions of
years.
Energetically unfavorable reactions, by contrast, create order in the
universe; they have a positive ΔG. Such reactions—for example, the
formation of a peptide bond between two amino acids—cannot occur
spontaneously; they take place only when they are coupled to a second
reaction with a negative ΔG large enough that the net ΔG of the entire
process is negative (Figure 3–17). Life is possible because enzymes can
create biological order by coupling energetically unfavorable reactions
with energetically favorable ones. These critical concepts are summarized, with examples, in Panel 3–1 (pp. 96–97).
Y
ENERGETICALLY
FAVORABLE
REACTION
X
The free energy of Y
is greater than the free
energy of X. Therefore
ΔG is negative (< 0), and
the disorder of the
universe increases
during the reaction
Y X.
this reaction can occur spontaneously
Y
ENERGETICALLY
UNFAVORABLE
REACTION
X
If the reaction X Y
occurred, ΔG would
be positive (> 0), and
the universe would
become more
ordered.
this reaction can occur only if
it is coupled to a second,
energetically favorable reaction
Figure 3–16 Energetically favorable
reactions have a negative ΔG, whereas
energetically unfavorable reactions have
a positive ΔG.
93
94
Chapter 3
Energy, Catalysis, and Biosynthesis
ΔG Changes As a Reaction Proceeds Toward Equilibrium
C
Y
negative
ΔG
positive
ΔG
X
D
Figure 3–17 Reaction coupling can drive
an energetically unfavorable reaction. The
energetically unfavorable (ΔG > 0) reaction
X → Y cannot occur unless it is coupled to
an energetically favorable (ΔG < 0) reaction
C → D, such that the net free-energy
change for the coupled reactions is negative
(less than 0).
ECB4 e3.17/3.17
Question 3–3
Consider the analogy of the jiggling
box containing coins that was
described on page 85. The reaction,
the flipping of coins that either
face heads up (H) or tails up (T), is
described by the equation
H ↔ T, where the rate of the
forward reaction equals the rate of
the reverse reaction.
A. What are ΔG and ΔG° in this
analogy?
B. What corresponds to the
temperature at which the reaction
proceeds? What corresponds to the
activation energy of the reaction?
Assume you have an “enzyme,”
called jigglase, which catalyzes this
reaction. What would the effect of
jigglase be and what, mechanically,
might jigglase do in this analogy?
It’s easy to see how a tensed spring, when left to itself, will relax and
release its stored energy to the environment as heat. But chemical
reactions are a bit more complex—and harder to intuit. That’s because
whether a reaction will proceed depends not only on the energy stored
in each individual molecule, but also on the concentrations of the molecules in the reaction mixture. Recalling our coin analogy, more coins
in a jiggling box will flip from a head to a tail orientation when the box
contains 90 heads and 10 tails, than when the box contains 10 heads and
90 tails.
The same is true for a chemical reaction. As the energetically favorable
reaction Y → X proceeds, the concentration of the product X will increase
and the concentration of the substrate Y will decrease. This change in
relative concentrations of substrate and product will cause the ratio of Y
to X to shrink, making the initially favorable ΔG less and less negative.
Unless more Y is added, the reaction will slow and eventually stop.
Because ΔG changes as products accumulate and substrates are depleted,
chemical reactions will generally proceed until they reach a state of
equilibrium. At that point, the rates of the forward and reverse reactions
are equal, and there is no further net change in the concentrations of
substrate or product (Figure 3–18). For reactions at chemical equilibrium,
ΔG = 0, so the reaction will not proceed forward or backward, and no
work can be done.
Such a state of chemical inactivity would be incompatible with life. Living
cells avoid reaching a state of complete chemical equilibrium because
they are constantly exchanging materials with their environment: replenishing nutrients and eliminating waste products. Many of the individual
reactions in the cell’s complex metabolic network also exist in disequilibrium because the products of one reaction are continually being siphoned
off to become the substrates in a subsequent reaction. Rarely do products
and substrates reach concentrations at which the forward and reverse
reaction rates are equal.
The Standard Free-Energy Change, ΔG°, Makes it Possible
to Compare the Energetics of Different Reactions
Because ΔG depends on the concentrations of the molecules in the reaction mixture at any given time, it is not a particularly useful value for
comparing the relative energies of different types of reactions. But such
energetic assessments are necessary, for example, to predict whether an
energetically favorable reaction is likely to have a ΔG negative enough
to drive an energetically unfavorable reaction. To compare reactions in
this way, we need to turn to the standard free-energy change of a reaction,
ΔG°. The ΔG° is independent of concentration; it depends only on the
intrinsic characters of the reacting molecules, based on their behavior
under ideal conditions where the concentrations of all the reactants are
set to the same fixed value of 1 mole/liter.
A large body of thermodynamic data has been collected from which ΔG°
can be calculated for most metabolic reactions. Some common reactions
are compared in terms of their ΔG° in Panel 3–1 (pp. 96–97).
The ΔG of a reaction can be calculated from ΔG° if the concentrations of
the reactants and products are known. For the simple reaction Y → X,
their relationship follows this equation:
[X]
ΔG = ΔG° + RT ln
[Y]
where ΔG is in kilocalories per mole, [Y] and [X] denote the concentrations
Free Energy and Catalysis
Figure 3–18 Reactions will eventually
reach a chemical equilibrium. At that
point, the forward and the backward
fluxes of reacting molecules are equal and
opposite. The widths of the arrows indicate
the relative rates at which an individual
molecule converts.
FOR THE ENERGETICALLY FAVORABLE REACTION Y → X,
Y
X
when X and Y are at equal concentrations, [Y] = [X], the formation of X
is energetically favored. In other words, the ΔG of Y → X is negative and
the ΔG of X → Y is positive. But because of thermal bombardments,
there will always be some X converting to Y.
THUS, FOR EACH INDIVIDUAL MOLECULE,
Y
X
X
Y
Therefore the ratio of X to Y
molecules will increase
conversion of
Y to X will
occur often.
Conversion of X to Y
will occur less often
than the transition
Y → X, because it
requires a more
energetic collision.
EVENTUALLY, there will be a large enough excess of X over Y to just
compensate for the slow rate of X → Y, such that the number of Y molecules
being converted to X molecules each second is exactly equal to the number
of X molecules being converted to Y molecules each second. At this point,
the reaction will be at equilibrium.
Y
AT EQUILIBRIUM,
X
there is no net change in the ratio of Y to X, and the
ΔG for both forward and backward reactions is zero.
of Y and X in moles/liter, ln is the natural logarithm, and RT is the product of the gas constant, R, and the absolute temperature, T. At 37°C,
RT = 0.616. (A mole is 6 × 1023 molecules of a substance.)
From this equation, we can see that when the concentrations of reactants and products are equal, in other words, [X]/[Y] = 1, the value of ΔG
equals the value of ΔG° (because ln 1 = 0). Thus when the reactants and
ECB4 e3.18/3.18
products are present in equal
concentrations, the direction of the reaction depends entirely on the intrinsic properties of the molecules.
The Equilibrium Constant Is Directly Proportional to ΔG°
As mentioned earlier, all chemical reactions tend to proceed toward
equilibrium. Knowing where that equilibrium lies for any given reaction
will tell you which way the reaction will proceed—and how far it will
go. For example, if a reaction is at equilibrium when the concentration
of the product is ten times the concentration of the substrate, and we
begin with a surplus of substrate and little or no product, the reaction
will proceed forward for some time. For the simple reaction Y → X, that
value—the ratio of substrate to product at equilibrium—is called the reaction’s equilibrium constant, K. Expressed as an equation:
[X]
K=
[Y]
where [X] is the concentration of the product and [Y] is the concentration
of the substrate at equilibrium.
95
Panel 3–1
FREE ENERGY AND BIOLOGICAL REACTIONS
FREE ENERGY
ΔG (“DELTA G”)
This panel reviews the concept of free energy and offers
examples showing how changes in free energy determine
whether—and how—biological reactions occur.
The molecules of a living cell possess energy because of their
vibrations, rotations, and movement through space, and
because of the energy that is stored in the bonds between
individual atoms.
Changes in free energy occurring in a reaction are
denoted by ΔG, where “Δ” indicates a difference. Thus,
for the reaction
A+B
C+D
ΔG = free energy (C + D) minus free energy (A + B)
ΔG measures the amount of disorder caused by a
reaction: the change in order inside the cell, plus the
change in order of the surroundings caused by the heat
released.
The free energy, G (in kcal/mole), measures the energy of a
molecule which could in principle be used to do useful work at
constant temperature, as in a living cell. Energy can also be
expressed in joules (1 cal = 4.184 joules).
REACTIONS CAUSE DISORDER
Think of a chemical reaction occurring in a cell that has a
constant temperature and volume. This reaction can produce
disorder in two ways.
1
heat
cell
2
ΔG is useful because it measures how far away from
equilibrium a reaction is. Thus the reaction
ATP
ADP
+
Pi
has a large negative ΔG because cells keep the reaction
a long way from equilibrium by continually making fresh
ATP. However, if the cell dies, then most of its ATP will be
hydrolyzed, until equilibrium is reached; at equilibrium,
the forward and backward reactions occur at equal rates
and ΔG = 0.
Changes of bond energy of the reacting molecules can
cause heat to be released, which disorders the environment
around the cell.
The reaction can decrease the amount of order in the
cell—for example, by breaking apart a long
chain of molecules, or by disrupting an interaction that
prevents bond rotations.
SPONTANEOUS REACTIONS
From the second law of thermodynamics, we know
that the disorder of the universe can only increase. ΔG
is negative if the disorder of the universe (reaction plus
surroundings) increases.
In other words, a chemical reaction that occurs
spontaneously must have a negative ΔG:
Gproducts – Greactants = ΔG < 0
EXAMPLE: The difference in free energy of 100 ml of
10 mM sucrose (common sugar) and 100 ml of 10 mM
glucose plus 10 mM fructose is about –5.5 calories.
Therefore, the hydrolysis reaction that produces two
monosaccharides from a disaccharide (sucrose →
glucose + fructose) can proceed spontaneously.
cell
PREDICTING REACTIONS
To predict the outcome of a reaction (Will it proceed to the
right or to the left? At what point will it stop?), we must
measure its standard free-energy change (ΔG o ).
This quantity represents the gain or loss of free energy as one
mole of reactant is converted to one mole of product under
“standard conditions” (all molecules present at a
concentration of 1 M and pH 7.0).
driving force
96
–5.5 cal
ΔG o for some reactions
glucose-1-P
sucrose
ATP
glucose-6-P
glucose + fructose
ADP + Pi
glucose + 6O2
–1.7 kcal/mole
–5.5 kcal/mole
–7.3 kcal/mole
6CO2 + 6H2O
–686 kcal/mole
sucrose
glucose +
fructose
In contrast, the reverse reaction (glucose + fructose →
sucrose), which has a ΔG of +5.5 calories, could not
occur without an input of energy from a coupled
reaction.
Free Energy and Catalysis
97
REACTION RATES
COUPLED REACTIONS
A spontaneous reaction is not necessarily an instantaneous
reaction: a reaction with a negative free-energy change (ΔG )
will not necessarily occur rapidly by itself. Consider, for
example, the combustion of glucose in oxygen:
Reactions can be “coupled” together if they share one or
more intermediates. In this case, the overall free-energy
change is simply the sum of the individual ΔG o values. A
reaction that is unfavorable (has a positive ΔG o ) can for this
reason be driven by a second, highly favorable reaction.
SINGLE REACTION
CH2OH
H C
O OH
C
H C
OH
HO C
H
C
H
6CO2 + 6H2O
+ 6O2
ΔG o =
+
+5.5 kcal/mole
glucose
fructose
NET RESULT: reaction will not occur
OH
o
ΔG = –686 kcal/mole
ATP
Even this highly favorable reaction may not occur for centuries
unless there are enzymes to speed up the process.
Enzymes are able to catalyze reactions and speed up their rate,
but they cannot change the ΔG o of a reaction.
ADP
P
ATP
P
will proceed until the ratio of concentrations [X]/[Y] is
equal to K (note: square brackets [ ] indicate
concentration). At this point, the free energy of the
system will have its lowest value.
free
energy
of system
+
fructose
NET RESULT:
A
[X]
[Y]
ΔG o = –1.42 log10K
(see text, p. 98)
/1.42
For example, the reaction
O
O
P
B
5.5 – 7.3 =
–1.8 kcal/mole
sucrose is made in a reaction driven
by the hydrolysis of ATP
hydrolysis
A
OH + H
O
B
The ΔG o for this reaction is sometimes loosely termed
the “bond energy.” Compounds such as acetyl
phosphate and ATP, which have a large negative ΔG o
of hydrolysis in an aqueous solution, are said to have
“high-energy” bonds.
ΔG o
(kcal/mole)
OH
acetyl P
glucose-1-P
P
sucrose
CH2O P
CH2OH
+
ΔG o =
HIGH-ENERGY BONDS
lowest
free
energy
o
ADP
One of the most common reactions in the cell is
hydrolysis, in which a covalent bond is split by adding
water.
equilibrium
point
K = 10–ΔG
+
glucose-1-P
glucose-1-P
A fixed relationship exists between the standard
free-energy change of a reaction, ΔG o, and its equilibrium
constant K. For example, the reversible reaction
Y
X
o
DG = –7.3 kcal/mole
P
COUPLED REACTIONS
+
CHEMICAL EQUILIBRIA
+
NET RESULT: reaction is highly favorable
glucose
At 37oC,
sucrose
glucose-6-P
ATP
acetate +
Pi
–10.3
ADP
Pi
–7.3
Pi
–3.3
+
has ΔG o = –1.74 kcal/mole. Therefore, its equilibrium
constant
K = 10(1.74/1.42) = 10(1.23) = 17
glucose-6-P
So the reaction will reach steady state when
[glucose-6-P]/[glucose-1-P] = 17
(Note that, for simplicity, H2O is omitted from the above
equations.)
glucose +
98
Chapter 3
Energy, Catalysis, and Biosynthesis
But how do we know at what concentrations of substrate and product a
reaction will reach equilibrium? It goes back to the intrinsic properties of
the molecules involved, as expressed by ΔG°. Let’s see why.
At equilibrium, the rate of the forward reaction is exactly balanced by
the rate of the reverse reaction. At that point, ΔG = 0, and there is no net
change of free energy to drive the reaction in either direction (see Panel
3–1, pp. 96–97).
Now, if we return to the equation presented on p. 94,
ΔG = ΔG° + RT ln
[X]
[Y]
we can see that, at equilibrium at 37°C, where ΔG = 0 and the constant
RT = 0.616, this equation becomes:
ΔG° = –0.616 ln
[X]
[Y]
In other words, ΔG° is directly proportional to the equilibrium constant, K:
ΔG° = –0.616 ln K
If we convert this equation from natural log (ln) to the more commonly
used base–10 logarithm (log), we get
ΔG° = –1.42 log K
Table 3–1 Relationship
Between the Standard FreeEnergy Change, ΔG°, and the
Equilibrium Constant
Equilibrium
Constant
[X]
[Y]
Standard Free Energy
(ΔG°) of X minus Free
Energy of Y in kcal/
mole
105
–7.1
104
–5.7
103
–4.3
102
–2.8
10
–1.4
1
0
10–1
1.4
10–2
2.8
10–3
4.3
10–4
5.7
10–5
7.1
Values of the equilibrium constant were
calculated for the simple chemical reaction
Y ↔ X, using the equation given in the text.
The ΔG° values given here are in kilocalories
per mole at 37°C. As explained in the text,
ΔG° represents the free-energy difference
under standard conditions (where all
components are present at a concentration
of 1 mole/liter).
From this table, we see that, if there is a
favorable free-energy change of
–4.3 kcal/mole for the transition Y → X,
there will be 1000 times more molecules
of X than of Y at equilibrium.
This equation reveals how the equilibrium ratio of Y to X, expressed as
the equilibrium constant K, depends on the intrinsic character of the
molecules, as expressed in the value of ΔG° (Table 3–1). It tells us that
for every 1.42 kcal/mole difference in free energy at 37°C, the equilibrium constant changes by a factor of 10. Thus, the more energetically
favorable the reaction, the more product will accumulate if the reaction
proceeds to equilibrium.
In Complex Reactions, the Equilibrium Constant Includes
the Concentrations of All Reactants and Products
We have so far discussed the simplest of reactions, Y → X, in which a
single substrate is converted into a single product. But inside cells, it is
more common for two reactants to combine to form a single product:
AB. How can we predict how this reaction will proceed?
A+B
The same principles apply, except that in this case the equilibrium constant K includes the concentrations of both of the reactants, in addition
to the concentration of the product:
K = [AB]/[A][B]
As illustrated in Figure 3–19, the concentrations of both reactants are
multiplied because the formation of product AB depends on the collision
of A and B, and these encounters occur at a rate that is proportional to
[A] × [B]. As with single-substrate reactions, ΔG° = –1.42 log K at 37°C.
The Equilibrium Constant Indicates the Strength of
Molecular Interactions
The concept of free-energy change does not only apply to chemical reactions where covalent bonds are being broken and formed, but also to
interactions where one molecule binds to another by means of noncovalent interactions (see Chapter 2, p. 63). Noncovalent interactions are
immensely important to cells. They include the binding of substrates to
enzymes, the binding of gene regulatory proteins to DNA, and the binding of one protein to another to make the many different structural and
functional protein complexes that operate in a living cell.
Free Energy and Catalysis
A
+
B
association
A B
association = association x concentration x concentration
rate constant
of A
of B
rate
association rate = kon [A] [B]
A B
dissociation
A
+
B
dissociation rate = dissociation x concentration
rate constant
of AB
dissociation rate = koff [AB]
AT EQUILIBRIUM:
association rate = dissociation rate
kon [A] [B]
[AB]
[A] [B]
=
kon
koff
=
koff [AB]
= K = equilibrium constant
Figure 3–19 The equilibrium constant (K)
for the reaction A + B → AB depends on
both the association and dissociation rate
constants. Molecules A and B must collide
in order to interact, and the association
rate is therefore proportional to the
product of their individual concentrations
[A] × [B]. As shown, the ratio of the rate
constants kon and koff for the association
and the dissociation reactions, respectively,
is equal to the equilibrium constant, K,
for the interaction. For two interacting
components, K involves the concentrations
of both substrates, in addition to that of the
product. However, the relationship between
K and ΔG° is the same as that shown in
Table 3–1. The larger the value of K, the
stronger is the binding between A and B.
Two molecules will bind to each other if the free-energy change for the
interaction is negative; that is, the free energy of the resulting complex is
lower than the sum of the free energies of the two partners when unbound.
Because the equilibrium constant
of a reaction is related directly to ΔG°,
ECB4 e3.19/3.19
K is commonly employed as a measure of the binding strength of a noncovalent interaction between two molecules. The binding strength is a
very useful quantity to know because it also indicates how specific the
interaction is between the two molecules.
Consider the reaction that was shown in Figure 3–19, where molecule A
interacts with molecule B to form the complex AB. The reaction proceeds
until it reaches equilibrium, at which point the number of association
events precisely equals the number of dissociation events; at this point,
the concentrations of reactants A and B, and of the complex AB, can be
used to determine the equilibrium constant K.
K becomes larger as the binding energy—that is, the energy released in
the binding interaction—increases. In other words, the larger K is, the
greater is the drop in free energy between the dissociated and associated states, and the more tightly the two molecules will bind. Even a
change of a few noncovalent bonds can have a striking effect on a binding interaction, as illustrated in Figure 3–20. In this example, eliminating
a few hydrogen bonds from a binding interaction can be seen to cause a
dramatic decrease in the amount of complex that exists at equilibrium.
For Sequential Reactions, the Changes in Free Energy Are
Additive
Now we return to our original concern: how can enzymes catalyze reactions that are energetically unfavorable? One way they do so is by directly
coupling energetically unfavorable reactions with energetically favorable
ones. Consider, for example, two sequential reactions,
X → Y and Y → Z
where the ΔG° values are +5 and –13 kcal/mole, respectively. (Recall that
a mole is 6 × 1023 molecules of a substance.) The unfavorable reaction,
X → Y, will not occur spontaneously. However, it can be driven by the
favorable reaction Y → Z, provided that the second reaction follows
the first. That’s because the overall free-energy change for the coupled
reaction is equal to the sum of the free-energy changes for each individual reaction. In this case, the ΔG° for the coupled reaction will be
–8 kcal/mole, making the overall pathway energetically favorable.
Consider 1000 molecules of A and 1000
molecules of B in the cytosol of a eukaryotic
cell. The concentration of both will be
about 10–9 M.
If the equilibrium constant (K ) for
A + B ↔ AB is 1010 liters/mole, then at
equilibrium there will be
270
270
A
B
molecules molecules
730
AB
complexes
If the equilibrium constant is a little weaker,
say 108 liters/mole—a value that represents a
loss of 2.8 kcal/mole of binding energy from
the example above, or 2–3 fewer hydrogen
bonds—then there will be
915
915
A
B
molecules molecules
85
AB
complexes
Figure 3–20 Small changes in the
number of weak bonds can have drastic
effects on a binding interaction. This
example illustrates the dramatic effect of
ECB4 e3.20/3.20
the presence or absence of a few weak
noncovalent bonds in the interaction
between two cytosolic proteins.
99
100
Chapter 3
Energy, Catalysis, and Biosynthesis
Cells can therefore cause the energetically unfavorable transition,
X → Y, to occur if an enzyme catalyzing the X → Y reaction is supplemented
by a second enzyme that catalyzes the energetically favorable reaction,
Y → Z. In effect, the reaction Y → Z acts as a “siphon,” pulling the conversion of all of molecule X to molecule Y, and then to molecule Z (Figure
3–21). For example, several of the reactions in the long pathway that
converts sugars into CO2 and H2O are energetically unfavorable. The
pathway nevertheless proceeds rapidly to completion, however, because
the total ΔG° for the series of sequential reactions has a large negative
value.
Question 3–4
For the reactions shown in Figure
3–21, sketch an energy diagram
similar to that in Figure 3–12 for
the two reactions alone and for
the combined reactions. Indicate
the standard free-energy changes
for the reactions X → Y, Y → Z,
and X → Z in the graph. Indicate
how enzymes that catalyze these
reactions would change the energy
diagram.
Figure 3–21 An energetically unfavorable
reaction can be driven by an energetically
favorable follow-on reaction that acts
as a chemical siphon. (A) At equilibrium,
there are twice as many X molecules as
Y molecules. (B) At equilibrium, there are
25 times more Z molecules than Y
molecules. (C) If the reactions in (A) and (B)
are coupled, nearly all of the X molecules
will be converted to Z molecules, as shown.
In terms of energetics, the ΔG° of the
Y → Z reaction is so negative that, when
coupled to the X → Y reaction, it lowers
the ΔG of X → Y, because the ΔG of X → Y
decreases as the ratio of Y to X declines. As
shown in Figure 3–18, arrow widths reflect
the relative rates at which an individual
molecule converts; the arrow lengths are the
same in both directions here, indicating that
there is no net flux.
Forming a sequential pathway, however, is not the answer for all metabolic needs. Often the desired reaction is simply X → Y, without further
conversion of Y to some other product. Fortunately, there are other, more
general ways of using enzymes to couple reactions together, involving
the production of activated carriers that can shuttle energy from one
reaction site to another. We discuss these systems shortly. Before we do,
let’s pause to look at how enzymes find and recognize their substrates
and how enzyme-catalyzed reactions proceed. After all, thermodynamic
considerations merely establish whether chemical reactions can occur;
enzymes actually make them happen.
Thermal Motion Allows Enzymes to Find Their Substrates
Enzymes and their substrates are both present in relatively small amounts
in the cytosol of a cell, yet a typical enzyme can capture and process
about a thousand substrate molecules every second. This means that an
enzyme can release its product and bind a new substrate in a fraction of
a millisecond. How do these molecules find each other so quickly in the
crowded cytosol of the cell?
Rapid binding is possible because molecular motions are enormously
fast. Because of heat energy, molecules are in constant motion and consequently will explore the cytosolic space very efficiently by wandering
X
Y
Y
equilibrium point for
X → Y reaction
(A)
Z
equilibrium point for
Y → Z reaction
(B)
X
Y
Z
(C)
equilibrium point for the coupled reaction X → Y → Z
Free Energy and Catalysis
Figure 3–22 A molecule traverses the cytosol by taking a random
walk. Molecules in solution move in a random fashion due to the
continual buffeting they receive in collisions with other molecules. This
movement allows small molecules to diffuse rapidly throughout the
cell cytosol (Movie 3.2).
randomly through it—a process called diffusion. In this way, every molecule in the cytosol collides with a huge number of other molecules each
second. As the molecules in a liquid collide and bounce off one another,
an individual molecule moves first one way and then another, its path
constituting a random walk (Figure 3–22).
Although the cytosol of a cell is densely packed with molecules of various shapes and sizes (Figure 3–23), experiments in which fluorescent
dyes and other labeled molecules are injected into the cell cytosol show
that small organic molecules diffuse through this aqueous gel nearly as
rapidly as they do through water. A small organic molecule, such as a
substrate, takes only about one-fifth of a second on average to diffuse a
distance of 10 μm. Diffusion is therefore an efficient way for small molecules to move limited distances in the cell.
Because proteins diffuse through the cytosol much more slowly than do
small molecules, the rate at which an enzyme will encounter its substrate depends on the concentration of the substrate. The most abundant
substrates are present in the cell at a concentration of about 0.5 mM.
Because pure water is 55 M, there is only about one such substrate molecule in the cell for every 105 water molecules. Nevertheless, the site on
an enzyme that binds this substrate will be bombarded by about 500,000
random collisions with the substrate every second. For a substrate concentration tenfold lower (0.05 mM), the number of collisions drops to
50,000 per second, and so on.
The random encounters between an enzyme and its substrate often lead
to the formation of an enzyme–substrate complex. This association is
stabilized by the formation of multiple, weak bonds between the enzyme
and substrate. These weak interactions—which can include hydrogen
bonds, van der Waals attractions, and electrostatic attractions (discussed
in Chapter 2)—persist until random thermal motion causes the molecules
to dissociate again. When two colliding molecules have poorly matching surfaces, few noncovalent bonds are formed, and their total energy
is negligible compared with that of thermal motion. In this case, the two
molecules dissociate as rapidly as they come together (see Figure 2–33).
This is what prevents incorrect and unwanted associations from forming between mismatched molecules, such as those between an enzyme
and the wrong substrate. But when the enzyme and substrate are well
matched, they form many weak interactions, which keep them held
together long enough for a covalent bond in the substrate molecule to
be formed or broken. Knowing the speed at which molecules collide and
come apart, as well as how fast bonds can be formed and broken, makes
the observed rate of enzymatic catalysis seem a little less amazing.
Figure 3–23 The cytosol is crowded with various molecules. Only
the macromolecules, which are drawn to scale, are shown. RNAs are
blue, ribosomes are green, and proteins are red. Enzymes and other
macromolecules diffuse relatively slowly in the cytosol, in part because
they interact with so many other macromolecules. Small molecules,
by contrast, can diffuse nearly as rapidly as they do in water. (Adapted
from D.S. Goodsell, Trends Biochem. Sci. 16:203–206, 1991. With
permission from Elsevier.)
net distance
traveled
ECB4 e3.22/3.22
Question 3–5
The enzyme carbonic anhydrase
is one of the speediest enzymes
known. It catalyzes the rapid
conversion of CO2 gas into the
much more soluble bicarbonate ion
(HCO3–). The reaction:
CO2 + H2O ↔ HCO3– + H+
is very important for the efficient
transport of CO2 from tissue, where
CO2 is produced by respiration,
to the lungs, where it is exhaled.
Carbonic anhydrase accelerates the
reaction 107-fold, hydrating 105 CO2
molecules per second at its maximal
speed. What do you suppose limits
the speed of the enzyme? Sketch
a diagram analogous to the one
shown in Figure 3–13 and indicate
which portion of your diagram has
been designed to display the
107-fold acceleration.
100 nm
ECB4 e3.23/3.23
101
Chapter 3
Energy, Catalysis, and Biosynthesis
Vmax and KM Measure Enzyme Performance
To catalyze a reaction, an enzyme must first bind its substrate. The substrate then undergoes a reaction to form the product, which initially
remains bound to the enzyme. Finally, the product is released and diffuses away, leaving the enzyme free to bind another substrate molecule
and catalyze another reaction (see Figure 3–15). The rates of the different
steps vary widely from one enzyme to another, and they can be measured by mixing purified enzymes and substrates together under carefully
defined conditions in a test tube (see How We Know, pp. 104–106).
In such experiments, the substrate is introduced in increasing concentrations to a solution containing a fixed concentration of enzyme. At first,
the concentration of the enzyme–substrate complex—and therefore the
rate at which product is formed—rises in a linear fashion in direct proportion to substrate concentration. However, as more and more enzyme
molecules become occupied by substrate, this rate increase tapers off,
until at a very high concentration of substrate it reaches a maximum
value, termed Vmax. At this point, the active sites of all enzyme molecules
in the sample are fully occupied by substrate, and the rate of product formation depends only on how rapidly the substrate molecule can undergo
a reaction to form the product. For many enzymes, this turnover number
is of the order of 1000 substrate molecules per second, although turnover
numbers between 1 and 100,000 have been measured.
Question 3–6
In cells, an enzyme catalyzes
the reaction AB → A + B. It was
isolated, however, as an enzyme that
carries out the opposite reaction
A + B → AB. Explain the paradox.
Because there is no clearly defined substrate concentration at which the
enzyme can be deemed fully occupied, biochemists instead use a different parameter to gauge the concentration of substrate needed to make
the enzyme work efficiently. This value is called the Michaelis constant,
KM, named after one of the biochemists who worked out the relationship. The KM of an enzyme is defined as the concentration of substrate
at which the enzyme works at half its maximum speed (Figure 3–24). In
general, a small KM indicates that a substrate binds very tightly to the
enzyme, and a large KM indicates weak binding.
Although an enzyme (or any catalyst) functions to lower the activation
energy for a reaction such as Y → X, it is important to note that the
enzyme will also lower the activation energy for the reverse reaction
X → Y to exactly the same degree. The forward and backward reactions
will therefore be accelerated by the same factor by an enzyme, and the
equilibrium point for the reaction—and thus its ΔG°—remains unchanged
(Figure 3–25).
Vmax
rate of reaction
102
½Vmax
KM
substrate concentration
Figure 3–24 An enzyme’s performance depends on how rapidly it can process
its substrate. The rate of an enzyme reaction (V ) increases as the substrate
concentration increases, until a maximum value (Vmax) is reached. At this point, all
substrate-binding sites on the enzyme molecules are fully occupied, and the rate
of the reaction is limited by the rate of the catalytic process on the enzyme surface.
For most enzymes, the concentration of substrate at which the reaction rate is halfmaximal (KM) is a direct measure of how tightly the substrate is bound, with a large
value of KM (a large amount of substrate needed) corresponding to weak binding.
ECB4 e3.24/3.24
Activated Carriers and Biosynthesis
X
(A)
Y
UNCATALYZED REACTION
AT EQUILIBRIUM
Y
X
(B)
ENZYME-CATALYZED REACTION
AT EQUILIBRIUM
Activated Carriers and Biosynthesis
Figure 3–25 Enzymes cannot change
the equilibrium point for reactions.
Enzymes, like all catalysts, speed up the
forward and reverse rates of a reaction by
the same amount. Therefore, for both the
(A) uncatalyzed and (B) catalyzed reactions
shown here, the number of molecules
undergoing the transition X → Y is equal
to the number of molecules undergoing
the transition Y → X when the ratio of
Y molecules to X molecules is 3.5 to 1,
as illustrated. In other words, both the
catalyzed and uncatalyzed reactions will
eventually reach the same equilibrium point,
although the catalyzed reaction will reach
equilibrium faster.
The energy released by energetically favorable reactions such as the oxiECB4 e3.25/3.25
dation of food molecules must
be stored temporarily before it can be
used by cells to fuel energetically unfavorable reactions, such as the synthesis of all the other molecules needed by the cell. In most cases, the
energy is stored as chemical-bond energy in a set of activated carriers,
small organic molecules that contain one or more energy-rich covalent
bonds. These molecules diffuse rapidly and carry their bond energy from
the sites of energy generation to the sites where energy is used for biosynthesis or for other energy-requiring cell activities (Figure 3–26).
Activated carriers store energy in an easily exchangeable form, either
as a readily transferable chemical group or as readily transferable (“high
energy”) electrons. They can serve a dual role as a source of both energy
and chemical groups for biosynthetic reactions. The most important activated carriers are ATP and two molecules that are closely related to each
other, NADH and NADPH. Cells use activated carriers like money to pay
for the energetically unfavorable reactions that otherwise would not take
place.
The Formation of an Activated Carrier Is Coupled to an
Energetically Favorable Reaction
When a fuel molecule such as glucose is oxidized in a cell, enzyme-catalyzed reactions ensure that a large part of the free energy released is
captured in a chemically useful form, rather than being released wastefully as heat. (Oxidizing sugar in a cell allows you to power metabolic
reactions, whereas burning a chocolate bar in the street will get you
nowhere, producing no metabolically useful energy.) In cells, energy
capture is achieved by means of a coupled reaction, in which an energetically favorable reaction is used to drive an energetically unfavorable
one that produces an activated carrier or some other useful molecule.
ENERGY
ENERGY
food
molecule
inactive carrier
energetically
favorable
reaction
new molecule
needed by cell
energetically
unfavorable
reaction
ENERGY
oxidized food
molecule
CATABOLISM
activated carrier
molecule
available in cell
ANABOLISM
103
Figure 3–26 Activated carriers can store
and transfer energy in a form that cells
can use. By serving as intracellular energy
shuttles, activated carriers perform their
function as go-betweens that link the
release of energy from the breakdown of
food molecules (catabolism) to the energyrequiring biosynthesis of small and large
organic molecules (anabolism).
104
How we Know
measuring enzyme performance
At first glance, it seems that a cell’s metabolic pathways
have been pretty well mapped out, with each reaction
proceeding predictably to the next—substrate X is converted to product Y, which is passed along to enzyme Z.
So why would anyone need to know exactly how tightly
a particular enzyme clutches its substrate or whether
it can process 100 or 1000 substrate molecules every
second?
In reality, such elaborate metabolic maps merely suggest which pathways a cell might follow as it converts
nutrients into small molecules, chemical energy, and the
larger building blocks of life. Like a road map, they do
not predict the density of traffic under a particular set
of conditions: which pathways the cell will use when it
is starving, when it is well fed, when oxygen is scarce,
when it is stressed, or when it decides to divide. The
study of an enzyme’s kinetics—how fast it operates, how
it handles its substrate, how its activity is controlled—
makes it possible to predict how an individual catalyst
will perform, and how it will interact with other enzymes
in a network. Such knowledge leads to a deeper understanding of cell biology, and it opens the door to learning
how to harness enzymes to perform desired reactions.
in the presence of different concentrations of substrate
(Figure 3–27A): the rate should increase as the amount
of substrate rises until the reaction reaches its Vmax. The
velocity of the reaction is measured by monitoring either
how quickly the substrate is consumed or how rapidly
the product accumulates. In many cases, the appearance of product or the disappearance of substrate can be
observed directly with a spectrophotometer. This instrument detects the presence of molecules that absorb light
at a particular wavelength; NADH, for example, absorbs
light at 340 nm, while its oxidized counterpart, NAD+,
does not. So, a reaction that generates NADH (by reducing NAD+) can be monitored by following the formation
of NADH at 340 nm in a spectrophotometer.
Speed
To determine the Vmax of a reaction, you would set up a
series of test tubes, where each tube contains a different
concentration of substrate. For each tube, add the same
amount of enzyme and then measure the velocity of the
reaction—the number of micromoles of substrate consumed or product generated per minute. Because these
numbers will tend to decrease over time, the rate used is
the velocity measured early in the reaction. These initial
velocity values (v) are then plotted against the substrate
concentration, yielding a curve like the one shown in
Figure 3–27B.
The first step to understanding how an enzyme performs
involves determining the maximal velocity, Vmax, for the
reaction it catalyzes. This is accomplished by measuring, in a test tube, how rapidly the reaction proceeds
Looking at this plot,
mine the exact value
the reaction rate will
this problem, the data
(B)
increasing [S]
v=
1/v (min/µmole)
(C)
v = initial rate of
substrate consumption
(µmole/min)
(A)
however, it is difficult to deterof Vmax, as it is not clear where
reach its plateau. To get around
are converted to their reciprocals
Vmax[S]
KM + [S]
–1/KM
[S] (µM)
1/v =
KM
Vmax
(1/[S]) + 1/Vmax
1/Vmax
1/[S] (µM–1)
Figure 3–27 Measured reaction rates are plotted to determine Vmax and KM of an enzyme-catalyzed reaction. (A) A series
of increasing substrate concentrations is prepared, a fixed amount of enzyme is added, and initial reaction rates (velocities) are
determined. (B) The initial velocities (v) plotted against the substrate concentrations [S] give a curve described by the general equation
y = ax/(b + x). Substituting our kinetic terms, the equation becomes v = Vmax[S]/(KM + [S]), where Vmax is the asymptote of the curve (the
value of y at an infinite value of x), and KM is equal to the substrate concentration where v is one-half Vmax. This is called the Michaelis–
Menten equation, named for the biochemists who provided evidence for this enzymatic relationship. (C) In a double-reciprocal plot, 1/v
is plotted against 1/[S]. The equation describing this straight line is 1/v = (KM/Vmax)(1/[S]) + 1/Vmax. When 1/[S] = 0, the y intercept (1/v)
is 1/Vmax. When 1/v = 0, the x intercept (1/[S]) is –1/KM. Plotting the data this way allows Vmax and KM to be calculated more precisely. By
convention, lowercase letters are used for variables (hence v for velocity) and uppercase letters are used for constants (hence Vmax).
105
and graphed in a “double-reciprocal plot,” where the
inverse of the velocity (1/v) appears on the y axis and
the inverse of the substrate concentration (1/[S]) on the
x axis (Figure 3–27C). This graph yields a straight line
whose y intercept (the point where the line crosses the
y axis) represents 1/Vmax and whose x intercept corresponds to –1/KM. These values are then converted to
values for Vmax and KM.
Enzymologists use this technique to determine the
kinetic parameters of many enzyme-catalyzed reactions
(although these days computer programs automatically
plot the data and spit out the sought-after values). Some
reactions, however, happen too fast to be monitored
in this way; the reaction is essentially complete—the
substrate entirely consumed—within thousandths of a
second. For these reactions, a special piece of equipment must be used to follow what happens during the
first few milliseconds after enzyme and substrate meet
(Figure 3–28).
Control
Substrates are not the only molecules that can influence how well or how quickly an enzyme works. In
many cases, products, substrate lookalikes, inhibitors,
and other small molecules can also increase or decrease
enzyme activity. Such regulation allows cells to control
when and how rapidly various reactions occur, a process we will consider in more detail in Chapter 4.
Determining how an inhibitor decreases an enzyme’s
activity can reveal how a metabolic pathway is regulated—and can suggest how those control points can be
circumvented by carefully designed mutations in specific
genes.
The effect of an inhibitor on an enzyme’s activity is monitored in the same way that we measured the enzyme’s
kinetics. A curve is first generated showing the velocity
of the uninhibited reaction between enzyme and substrate, as described previously. Additional curves are
then produced for reactions in which the inhibitor molecule has been included in the mix.
Comparing these curves, with and without inhibitor, can
also reveal how a particular inhibitor impedes enzyme
activity. For example, some inhibitors bind to the same
site on an enzyme as its substrate. These competitive
inhibitors block enzyme activity by competing directly
with the substrate for the enzyme’s attention. They
resemble the substrate enough to tie up the enzyme,
but they differ enough in structure to avoid getting converted to product. This blockage can be overcome by
adding enough substrate so that enzymes are more
likely to encounter a substrate molecule than an inhibitor molecule. From the kinetic data, we can see that
competitive inhibitors do not change the Vmax of a reaction; in other words, add enough substrate and the
enzyme will encounter mostly substrate molecules and
will reach its maximum velocity (Figure 3–29).
light source
mixer
enzyme
substrate
detector
Figure 3–28 A stopped-flow apparatus is used to observe reactions during the first few milliseconds. In this piece of equipment,
the enzyme and substrate are rapidly injected into a mixing chamber through two syringes. The enzyme and its substrate meet as they
shoot through the mixing tube at flow rates that can easily reach 1000 cm/sec. They then enter another tube and zoom past a detector
that monitors, say, the appearance of product. If the detector is located within a centimeter of where the enzyme and substrate meet, it
is possible to observe reactions when they are only a few milliseconds old.
ECB4 e3.27/3.27
106
(A)
(B)
enzyme
competitive
inhibitor
substrate
substrate
only
v
substrate
+ inhibitor
[S]
inactive
enzyme
active
enzyme
substrate
+ inhibitor
Figure 3–29 A competitive inhibitor directly blocks
substrate binding to an enzyme. (A) The active site of
the enzyme can bind either the competitive inhibitor or
the substrate, but not both together. (B) The upper plot
shows that inhibition by a competitive inhibitor can be
overcome by increasing the substrate concentration.
The double-reciprocal plot below shows that the Vmax
of the reaction is not changed in the presence of the
competitive inhibitor: the y intercept is identical for both
the curves.
1/v
products
substrate
1/[S]
Competitive inhibitors can be used to treat patients who
have been poisoned by ethylene glycol, an ingredient in
commercially available antifreeze. Although ethylene
glycol is itself not fatally toxic, a by-product of its metabolism—oxalic acid—can ECB4
be lethal.
To prevent oxalic acid
e3.28/3.28
from forming, the patient is given a large (though not
quite intoxicating) dose of ethanol. Ethanol competes
with the ethylene glycol for binding to alcohol dehydrogenase, the first enzyme in the pathway to oxalic acid
formation. As a result, the ethylene glycol goes mostly
unmetabolized and is safely eliminated from the body.
Other types of inhibitors may interact with sites on the
enzyme distant from where the substrate binds. As we
discuss in Chapter 4, many biosynthetic enzymes are
regulated by feedback inhibition, whereby an enzyme
early in a pathway will be shut down by a product generated later in the pathway. Because this type of inhibitor
binds to a separate regulatory site on the enzyme, the
substrate can still bind, but it might do so more slowly
than it would in the absence of inhibitor. Such noncompetitive inhibition is not overcome by the addition of
more substrate.
Design
With the kinetic data in hand, we can use computer
modeling programs to predict how an enzyme will perform, and even how a cell will respond when exposed
to different conditions—such as the addition of a particular sugar or amino acid to the culture medium, or
the addition of a poison or a pollutant. Seeing how a
cell manages its resources—which pathways it favors
for dealing with particular biochemical challenges—can
also suggest strategies for designing better catalysts for
reactions of medical or commercial importance (e.g.,
for producing drugs or detoxifying industrial waste).
Using such tactics, bacteria have even been genetically
engineered to produce large amounts of indigo—the
dye, originally extracted from plants, that makes your
blue jeans blue.
Computer programs have been developed to facilitate
the dissection of complex reaction pathways. They
require information about the components in the pathway, including the KM and Vmax of the participating
enzymes and the concentrations of enzymes, substrates,
products, inhibitors, and other regulatory molecules.
The program then predicts how molecules will flow
through the pathway, which products will be generated, and where any bottlenecks might be. The process
is not unlike balancing an algebraic equation, in which
every atom of carbon, nitrogen, oxygen, and so on must
be tallied. Such careful accounting makes it possible
to rationally design ways to manipulate the pathway,
such as re-routing it around a bottleneck, eliminating
an important inhibitor, redirecting the reactions to favor
the generation of predominantly one product, or extending the pathway to produce a novel molecule. Of course,
such computer models must be validated in cells, which
may not always behave as predicted.
Producing designer cells that spew out commercial
products generally requires using genetic engineering
techniques to introduce the gene or genes of choice into
a cell, usually a bacterium, that can be manipulated and
maintained in the laboratory. We discuss these methods
at greater length in Chapter 10. Harnessing the power of
cell biology for commercial purposes—even to produce
something as simple as the amino acid tryptophan—is
currently a multibillion-dollar industry. And, as more
genome data come in, presenting us with more enzymes
to exploit, it may not be long before vats of custom-made
bacteria are churning out drugs and chemicals that represent the biological equivalent of pure gold.
107
Activated Carriers and Biosynthesis
(A)
(B)
(C)
hydraulic
machine
heat
kinetic energy of falling rocks is
transformed into heat energy only
USEFUL
WORK
heat
part of the kinetic energy is used to lift
a bucket of water, and a correspondingly
smaller amount is transformed into heat
the potential energy stored in the
raised bucket of water can be used to
drive hydraulic machines that carry out
a variety of useful tasks
Figure 3–30 A mechanical model illustrates the principle of coupled chemical reactions. The spontaneous
reaction shown in (A) could serve as an analogy for the direct oxidation of glucose to CO2 and H2O, which produces
only heat. In (B), the same reaction is coupled to a second reaction, which could serve as an analogy for the synthesis
of activated carriers. The energy produced in (B) is in a more useful form than in (A) and can be used to drive a
variety of otherwise energetically unfavorable reactions (C).
Such coupling requires enzymes, which are fundamental to all of the
energy transactions in the cell.
The nature of a coupled reaction is illustrated by a mechanical analogy
in Figure 3–30, in which an energetically favorable chemical reaction
is represented by rocks falling from a cliff. The kinetic energy of falling
rocks would normally be entirely wasted in the form ECB4
of heat
generated by
e3.30/3.30
friction when the rocks hit the ground (Figure 3–30A). By careful design,
however, part of this energy could be used to drive a paddle wheel that
lifts a bucket of water (Figure 3–30B). Because the rocks can now reach
the ground only after moving the paddle wheel, we say that the energetically favorable reaction of rocks falling has been directly coupled to the
energetically unfavorable reaction of lifting the bucket of water. Because
part of the energy is used to do work in (B), the rocks hit the ground with
less velocity than in (A), and correspondingly less energy is wasted as
heat. The energy saved in the elevated bucket of water can then be used
to do useful work (Figure 3–30C).
Analogous processes occur in cells, where enzymes play the role of the
paddle wheel in Figure 3–30B. By mechanisms that we discuss in Chapter
13, enzymes couple an energetically favorable reaction, such as the oxidation of foodstuffs, to an energetically unfavorable reaction, such as the
generation of activated carriers. As a result, the amount of heat released
by the oxidation reaction is reduced by exactly the amount of energy that
is stored in the energy-rich covalent bonds of the activated carrier. That
saved energy can then be used to power a chemical reaction elsewhere
in the cell.
ATP Is the Most Widely Used Activated Carrier
The most important and versatile of the activated carriers in cells is ATP
(adenosine 5ʹ-triphosphate). Just as the energy stored in the raised bucket
of water in Figure 3–30B can be used to drive a wide variety of hydraulic
machines, ATP serves as a convenient and versatile store, or currency, of
energy that can be used to drive a variety of chemical reactions in cells.
Question 3–7
Use Figure 3–30B to illustrate the
following reaction driven by the
hydrolysis of ATP:
X + ATP → Y + ADP + Pi
A. In this case, which molecule or
molecules would be analogous to
(i) rocks at top of cliff, (ii) broken
debris at bottom of cliff, (iii) bucket
at its highest point, and (iv) bucket
on the ground?
B. What would be analogous to
(i) the rocks hitting the ground in
the absence of the paddle wheel in
Figure 3–30A and (ii) the hydraulic
machine in Figure 3–30C?
108
Chapter 3
Energy, Catalysis, and Biosynthesis
Figure 3–31 The interconversion of
ATP and ADP occurs in a cycle. The two
outermost phosphate groups in ATP are
held to the rest of the molecule by highenergy phosphoanhydride bonds and
are readily transferred to other organic
molecules. Water can be added to ATP to
form ADP and inorganic phosphate (Pi).
Inside a cell, this hydrolysis of the terminal
phosphate of ATP yields between 11 and
13 kcal/mole of usable energy. Although
the ΔGº of this reaction is –7.3 kcal/mole,
the ΔG is much more negative, because the
ratio of ATP to the products ADP and Pi is
so high inside the cell.
The large negative ΔGº of the reaction
arises from a number of factors. Release of
the terminal phosphate group removes an
unfavorable repulsion between adjacent
negative charges; in addition, the inorganic
phosphate ion (Pi) released is stabilized by
favorable hydrogen-bond formation with
water. The formation of ATP from ADP and
Pi reverses the hydrolysis reaction; because
this condensation reaction is energetically
unfavorable, it must be coupled to an
energetically more favorable reaction to
occur.
ATP
phosphoanhydride bonds
O
_
_
O
_
O
_
ADENINE
O P O P O P O CH2
O
O
O
RIBOSE
energy from
sunlight or from
the breakdown
of food
O
_
ΔGº < 0
ΔGº > 0
_
O P O
_
+
O
_
_
O
_
energy available
to drive energetically
unfavorable
reactions
ADENINE
O P O P O CH2
O
O
O
inorganic
phosphate ( Pi )
RIBOSE
ADP
As shown in Figure 3–31, ATP is synthesized in an energetically unfavorable phosphorylation reaction, in which a phosphate group is added
to ADP (adenosine 5ʹ-diphosphate). When required, ATP gives up this
energy packet in an energetically favorable hydrolysis to ADP and inorganic phosphate (Pi). The regenerated ADP is then available to be used
for another round of the phosphorylation reaction that forms ATP, creating an ATP cycle in the cell.
The energetically favorable reaction of ATP hydrolysis is coupled to
ECB4 e3.31/3.31
many otherwise unfavorable
reactions through which other molecules
are synthesized. We will encounter several of these reactions in this
chapter, where we will see exactly how this is done. ATP hydrolysis is
often coupled to the transfer of the terminal phosphate in ATP to another
molecule, as illustrated in Figure 3–32. Any reaction that involves the
transfer of a phosphate group to a molecule is termed a phosphorylation
reaction. Phosphorylation reactions are examples of condensation reactions (see Figure 2–25), and they occur in many important cell processes:
they activate substrates, mediate the exchange of chemical energy, and
serve as key constituents of intracellular signaling pathways (discussed
in Chapter 16).
hydroxyl
group on
another
molecule
O
_
Figure 3–32 The terminal phosphate
of ATP can be readily transferred to
other molecules. Because an energyrich phosphoanhydride bond in ATP
is converted to a less energy-rich
phosphoester bond in the phosphateaccepting molecule, this reaction is
energetically favorable, having a large
negative ΔGº (see Panel 3–1, pp. 96–97).
Phosphorylation reactions of this type are
involved in the synthesis of phospholipids
and in the initial steps of the breakdown of
sugars, as well as in many other metabolic
and intracellular signaling pathways.
HO C C
_
O
_
O
_
O
O
O
ATP
RIBOSE
phosphoanhydride
bond
ΔGº < 0
O
_
_
O P O C C
O
phosphoester
bond
ADENINE
O P O P O P O CH2
O
_
O
PHOSPHATE TRANSFER
_
ADENINE
_
+ O P O P O CH2
O
O
ADP
RIBOSE
Activated Carriers and Biosynthesis
ATP is the most abundant activated carrier in cells. It is used, for example,
to supply energy for many of the pumps that actively transport substances into or out of the cell (discussed in Chapter 12); it also powers the
molecular motors that enable muscle cells to contract and nerve cells to
transport materials along their lengthy axons (discussed in Chapter 17).
Why evolution selected this particular nucleotide over the others as the
major carrier of energy, however, remains a mystery. The nucleotide GTP,
although similar, has very different functions in the cell, as we discuss in
later chapters.
Energy Stored in ATP Is Often Harnessed to Join Two
Molecules Together
A common type of reaction that is needed for biosynthesis is one in which
two molecules, A and B, are joined together by a covalent bond to produce A–B in the energetically unfavorable condensation reaction:
A–H + B–OH → A–B + H2O
ATP hydrolysis can be coupled indirectly to this reaction to make it go
forward. In this case, energy from ATP hydrolysis is first used to convert B–OH to a higher-energy intermediate compound, which then reacts
directly with A–H to give A–B. The simplest mechanism involves the
transfer of a phosphate from ATP to B–OH to make B–O–PO3, in which
case the reaction pathway contains only two steps:
1. B–OH + ATP → B–O–PO3 + ADP
2. A–H + B–O–PO3 → A–B + Pi
Net result: B–OH + ATP + A–H → A–B + ADP + Pi
The condensation reaction, which by itself is energetically unfavorable, has been forced to occur by being coupled to ATP hydrolysis in an
enzyme-catalyzed reaction pathway (Figure 3–33A).
A biosynthetic reaction of exactly this type is employed to synthesize the
amino acid glutamine, as illustrated in Figure 3–33B. We will see later in
the chapter that very similar (but more complex) mechanisms are also
used to produce nearly all of the large molecules of the cell.
NADH and NADPH Are Both Activated Carriers of
Electrons
Other important activated carriers participate in oxidation–reduction
reactions and are commonly part of coupled reactions in cells. These
activated carriers are specialized to carry both high-energy electrons and
hydrogen atoms. The most important of these electron carriers are NADH
(nicotinamide adenine dinucleotide) and the closely related molecule
NADPH (nicotinamide adenine dinucleotide phosphate). Both NADH and
NADPH carry energy in the form of two high-energy electrons plus a proton (H+), which together form a hydride ion (H–). When these activated
carriers pass their energy (in the form of a hydride ion) to a donor molecule, they become oxidized to form NAD+ and NADP+, respectively.
Like ATP, NADPH is an activated carrier that participates in many
important biosynthetic reactions that would otherwise be energetically unfavorable. NADPH is produced according to the general scheme
shown in Figure 3–34A. During a special set of energy-yielding catabolic
reactions, a hydride ion is removed from the substrate molecule and
added to the nicotinamide ring of NADP+ to form NADPH. This is a typical oxidation–reduction reaction; the substrate is oxidized and NADP+ is
reduced.
Question 3–8
The phosphoanhydride bond that
links two phosphate groups in
ATP in a high-energy linkage has a
ΔG° of –7.3 kcal/mole. Hydrolysis
of this bond in a cell liberates from
11 to 13 kcal/mole of usable energy.
How can this be? Why do you think
a range of energies is given, rather
than a precise number as for ΔG°?
109
110
Chapter 3
Energy, Catalysis, and Biosynthesis
(A)
(B)
P
P
O
C
B
CH2
high-energy intermediate
H
CH2
A
H3N
ATP
ADP
Pi
CONDENSATION
STEP
+
CH
COO–
high-energy intermediate
ATP
ACTIVATION
STEP
B
O
O
OH
products of
ATP hydrolysis
A
B
ACTIVATION
STEP
OH
O
C
NH3
ammonia
ADP
Pi
products of
ATP hydrolysis
CONDENSATION
STEP
O
CH2
CH2
H3N
+
CH
NH2
C
CH2
COO–
glutamic acid
CH2
H3N
+
CH
COO–
glutamine
Figure 3–33 An energetically unfavorable biosynthetic reaction can be driven by ATP hydrolysis.
(A) Schematic illustration of the formation of A–B in the condensation reaction described in the text. (B) The
biosynthesis of the amino acid glutamine from glutamic acid. Glutamic acid is first converted to a high-energy
phosphorylated intermediate (corresponding to the compound B–O–PO3 described in the text), which then reacts
with ammonia (corresponding to A–H) to form glutamine. In this example, both steps occur on the surface of the
same enzyme, glutamine synthetase (not shown). For clarity, the glutamic acid side chain is shown in its uncharged
ECB4 e3.33/3.33
form. ATP hydrolysis can drive this energetically unfavorable reaction because it yields more energy (ΔG° of
–7.3 kcal/mole) than the energy required for the synthesis of glutamine from glutamic acid plus NH3 (ΔG°
of +3.4 kcal/mole).
The hydride ion carried by NADPH is given up readily in a subsequent
oxidation–reduction reaction, because the ring can achieve a more stable
arrangement of electrons without it. In this subsequent reaction, which
regenerates NADP+, the NADPH becomes oxidized and the substrate
becomes reduced—thus completing the NADPH cycle. NADPH is efficient
at donating its hydride ion to other molecules for the same reason that
ATP readily transfers a phosphate: in both cases, the transfer is accompanied by a large negative free-energy change. One example of the use of
NADPH in biosynthesis is shown in Figure 3–35.
NADPH and NADH Have Different Roles in Cells
NADPH and NADH differ in a single phosphate group, which is located far
from the region involved in electron transfer in NADPH (Figure 3–34B).
Although this phosphate group has no effect on the electron-transfer
properties of NADPH compared with NADH, it is nonetheless crucial
for their distinctive roles, as it gives NADPH a slightly different shape
from NADH. This subtle difference in conformation makes it possible for
the two carriers to bind as substrates to different sets of enzymes and
thereby deliver electrons (in the form of hydride ions) to different target
molecules.
Why should there be this division of labor? The answer lies in the need
to regulate two sets of electron-transfer reactions independently. NADPH
operates chiefly with enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological
molecules. NADH, by contrast, has a special role as an intermediate in
Activated Carriers and Biosynthesis
(A)
H
C
OH
NADP+
C
O
NADPH
H
C
H
C
C
+
C
+H
oxidation of
molecule 1
reduction of
molecule 2
(B)
NADP+
H
O
reduced form
H
+
N
C
NH2
O
H–
RIBOSE
N
P
O
NH2
O
RIBOSE
ADENINE
P
O
H
C
nicotinamide
ring
P
NADPH
oxidized form
111
Figure 3–34 NADPH is an
activated carrier of electrons.
(A) NADPH is produced in
reactions of the general type
shown on the left, in which two
hydrogen atoms are removed from
a substrate. The oxidized form
of the carrier molecule, NADP+,
receives one hydrogen atom plus
an electron (a hydride ion), while
the proton (H+) from the other
H atom is released into solution.
Because NADPH holds its hydride
ion in a high-energy linkage, the
ion can easily be transferred to
other molecules, as shown on the
right. (B) The structure of NADP+
and NADPH. On the left is a balland-stick model of NADP. The part
of the NADP+ molecule known as
the nicotinamide ring accepts two
electrons, together with a proton
(the equivalent of a hydride ion,
H–), forming NADPH. NAD+ and
NADH are identical in structure to
NADP+ and NADPH, respectively,
except that they lack the
phosphate group, as indicated.
ADENINE
P
O
RIBOSE
RIBOSE
O
O
P
P
7-dehydrocholesterol
phosphate group missing
+
in NAD and NADH
the catabolic system of reactions that generate ATP through the oxidation of food molecules, as we discuss in Chapter 13. The genesis of NADH
from NAD+ and that of NADPH from NADP+ occurs by different pathways
that are independently regulated, so that the cell can adjust the supply of
electrons for these two contrasting purposes. Inside the cell, the ratio of
NAD+ to NADH is kept high, whereas the ratio of NADP+ to NADPH is kept
low. This arrangement provides plenty of NAD+ to act as an oxidizing
agent and plenty of NADPH to act as a reducing agent—as required for
ECB4 e3.34/3.34
their special roles in catabolism and
anabolism, respectively.
C
C
HO
H
NADPH + H+
NADP+
Cells Make Use of Many Other Activated Carriers
In addition to ATP (which transfers a phosphate) and NADPH and NADH
(which transfer electrons and hydrogen), cells make use of other activated
carriers that pick up and carry a chemical group in an easily transferred,
high-energy linkage. FADH2, like NADH and NADPH, carries hydrogen and
high-energy electrons (see Figure 13–13B). But other important reactions
involve the transfers of acetyl, methyl, carboxyl, and glucose groups from
activated carriers for the purpose of biosynthesis (Table 3–2). Coenzyme
A, for example, can carry an acetyl group in a readily transferable linkage. This activated carrier, called acetyl CoA (acetyl coenzyme A), is
shown in Figure 3–36. It is used, for example, to add sequentially twocarbon units in the biosynthesis of the hydrocarbon tails of fatty acids.
C
HO
C
H
H
H
cholesterol
Figure 3–35 NADPH participates in the
final stage of one of the biosynthetic
routes leading to cholesterol. As in many
other biosynthetic reactions, the reduction
of the C=CECB4
bonde3.35/3.35
is achieved by the transfer
of a hydride ion from the activated carrier
NADPH, plus a proton (H+) from solution.
112
Chapter 3
Energy, Catalysis, and Biosynthesis
Table 3–2 Some Activated Carriers Widely Used in Metabolism
Activated Carrier
Group Carried in High-Energy Linkage
ATP
phosphate
NADH, NADPH, FADH2
electrons and hydrogens
Acetyl CoA
acetyl group
Carboxylated biotin
carboxyl group
S-adenosylmethionine
methyl group
Uridine diphosphate glucose
glucose
In acetyl CoA and the other activated carriers in Table 3–2, the transferable group makes up only a small part of the molecule. The rest consists
of a large organic portion that serves as a convenient “handle,” facilitating the recognition of the carrier molecule by specific enzymes. As with
acetyl CoA, this handle portion very often contains a nucleotide. This
curious fact may be a relic from an early stage of cell evolution. It is
thought that the main catalysts for early life forms on Earth were RNA
molecules (or their close relatives) and that proteins were a later evolutionary addition. It is therefore tempting to speculate that many of the
activated carriers that we find today originated in an earlier RNA world,
where their nucleotide portions would have been useful for binding these
carriers to RNA-based catalysts, or ribozymes (discussed in Chapter 7).
Activated carriers are usually generated in reactions coupled to ATP
hydrolysis, as shown for biotin in Figure 3–37. Therefore, the energy that
enables their groups to be used for biosynthesis ultimately comes from
the catabolic reactions that generate ATP. Similar processes occur in the
synthesis of the very large macromolecules—the nucleic acids, proteins,
and polysaccharides—which we discuss next.
acetyl
group
nucleotide
ADENINE
Figure 3–36 Acetyl coenzyme A (CoA) is
another important activated carrier.
A ball-and-stick model is shown above the
structure of acetyl CoA. The sulfur atom
(yellow) forms a thioester bond to acetate.
Because the thioester bond is a highenergy linkage, it releases a large amount
of free energy when it is hydrolyzed; thus
the acetyl group carried by CoA can be
readily transferred to other molecules.
H3C
H H
O H H
O H
C S C C N C C C N C C
O
high-energy
bond
H H H
H H H
CH3 H
O
O
C
C O P O P O CH2
OH CH3 H
O–
O–
RIBOSE
–O
acetyl group
Coenzyme A (CoA)
O
P O
O–
Activated Carriers and Biosynthesis
113
CARBOXYLATION OF BIOTIN
carboxylated
biotin
–
O
O
C
high-energy
bond
N
O
S
N
H
ADP
CH3
O
C O
ENZYME
O
Pi
C
–
O
pyruvate
ATP
biotin
–
O
O
S
C
OH
bicarbonate
H
N
O
O
–
C
O
CH2
N
H
C O
O
ENZYME
O
C
O–
oxaloacetate
pyruvate carboxylase
CARBOXYL GROUP TRANSFER
Figure 3–37 An activated carrier transfers a carboxyl group to a substrate. Biotin is a vitamin that is used by
a number of enzymes, including pyruvate carboxylase shown here. Once it is carboxylated, biotin can transfer a
carboxyl group to another molecule. Here, it transfers a carboxyl group to pyruvate, producing oxaloacetate, a
molecule needed in the citric acid cycle (discussed in Chapter 13). Other enzymes use biotin to transfer carboxyl
groups to other acceptor molecules. Note that the synthesis of carboxylated biotin requires energy derived from ATP
hydrolysis—a general feature of many activated carriers.
ECB4 e3.37/3.37
The Synthesis of Biological Polymers Requires an Energy
Input
The macromolecules of the cell constitute the vast majority of its dry
mass—that is, the mass not due to water. These molecules are made
from subunits (or monomers) that are linked together by bonds formed
during an enzyme-catalyzed condensation reaction. The reverse reaction—the breakdown of polymers—occurs through enzyme-catalyzed
hydrolysis reactions. These hydrolysis reactions are energetically favorable, whereas the corresponding biosynthetic reactions require an energy
input and are more complex (Figure 3–38).
The nucleic acids (DNA and RNA), proteins, and polysaccharides are all
polymers that are produced by the repeated addition of a subunit onto
one end of a growing chain. The mode of synthesis of each of these
macromolecules is outlined in Figure 3–39. As indicated, the condensation step in each case depends on energy provided by the hydrolysis of a
nucleoside triphosphate. And yet, except for the nucleic acids, there are
no phosphate groups left in the final product molecules. How, then, is the
energy of ATP hydrolysis coupled to polymer synthesis?
H2O
A
H + HO
B
CONDENSATION
energetically
unfavorable
H2O
A
B
HYDROLYSIS
energetically
favorable
A
H + HO
B
Figure 3–38 In cells, macromolecules are
synthesized by condensation reactions
and broken down by hydrolysis reactions.
Condensation reactions are all energetically
unfavorable, whereas hydrolysis reactions
are all energetically favorable.
114
Chapter 3
Energy, Catalysis, and Biosynthesis
(B) NUCLEIC ACIDS
(A) POLYSACCHARIDES
glucose
glycogen
CH2OH
O
CH2OH
O
CH2OH
O
OH
OH
OH
OH
HO
O
HO
CH2OH
O
OH
OH
O
OH
CH2
A
O
O
RNA
CH2OH
O
O
P
O
CH2
C
O
OH
H2O
OH
OH
energy from nucleoside
triphosphate hydrolysis
O
(C) PROTEINS
C
C
R
N
C
H
H
H
H
O
N
C
OH
H
C
R
O
P
O
C
C
R
O
P
_
_
CH2
O
G
O
C
nucleotide
CH2
O
G
OH
OH
RNA
OH
OH
energy from nucleoside
triphosphate hydrolysis
H2O
O
OH
O
O
OH
H
C
O
O
amino acid
R
_
O
OH
O
O
P
O
OH
protein
OH
O
_
O
CH2
OH
O
OH
O
glycogen
H
A
O
OH
CH2OH
O
HO
CH2
energy from nucleoside
triphosphate hydrolysis
H2O
O
O
OH
OH
O
R
O
N
C
C
H
H
H
N
C
H
R
O
C
OH
protein
Question 3–9
Which of the following reactions will
occur only if coupled to a second,
energetically favorable reaction?
A. glucose + O2 → CO2 + H2O
B. CO2 + H2O → glucose + O2
C. nucleoside triphosphates → DNA
D. nucleotide bases → nucleoside
triphosphates
E. ADP + Pi → ATP
Figure 3–39 The synthesis of macromolecules requires an input of energy.
Synthesis of a portion of (A) a polysaccharide, (B) a nucleic acid, and (C) a protein is
shown here. In each case, synthesis involves a condensation reaction in which water
is lost; the atoms involved are shaded in pink. Not shown is the consumption of
high-energy nucleoside triphosphates that is required to activate each subunit prior
to its addition. In contrast, the reverse reaction—the breakdown of all three types of
polymers—occurs through the simple addition of water, or hydrolysis (not shown).
For each type of macromolecule, an enzyme-catalyzed pathway exists,
which resembles that discussed previously for the synthesis of the amino
acid glutamine (see Figure 3–33). The principle is exactly the same, in
that the –OH group that will be removed in the condensation reaction is
first activated by forming a high-energy linkage to a second molecule.
The mechanisms used to link ATP hydrolysis to the synthesis of proteins
and polysaccharides, however, are more complex than that used for
ECB4 e3.39/3.39
glutamine synthesis. In the biosynthetic pathways leading to these macromolecules, a series of high-energy intermediates generates the final
high-energy bond that is broken during the condensation step (as discussed in Chapter 7 for protein synthesis).
There are limits to what each activated carrier can do in driving biosynthesis. For example, the ΔG for the hydrolysis of ATP to ADP and inorganic
phosphate (Pi) depends on the concentrations of all of the reactants, and
under the usual conditions in a cell, is between –11 and –13 kcal/mole.
In principle, this hydrolysis reaction can be used to drive an unfavorable
reaction with a ΔG of, perhaps, +10 kcal/mole, provided that a suitable
reaction path is available. For some biosynthetic reactions, however,
even –13 kcal/mole may be insufficient. In these cases, the path of ATP
Activated Carriers and Biosynthesis
(A)
Figure 3–40 In an alternative route for
the hydrolysis of ATP, pyrophosphate
is first formed and then hydrolyzed in
solution. This route releases about twice
as much free energy as the reaction shown
earlier in Figure 3–31. (A) In each of the two
successive hydrolysis reactions, an oxygen
atom from the participating water molecule
is retained in the products, whereas the
hydrogen atoms from water form free
hydrogen ions, H+. (B) The overall reaction
shown in summary form.
(B)
O
O
O
ADENINE
_
O P O P O P O CH2
_
O
O
_
ATP
_
O
RIBOSE
adenosine triphosphate (ATP)
H2O
H2O
O
O
O
_
O P O P O
_
_
+
_
O
ADENINE
O P O CH2
P Pi
_
_
115
+
AMP
O
O
RIBOSE
pyrophosphate
H2O
adenosine monophosphate (AMP)
H2O
O
O
_
O P OH
_
+
O P OH
_
PPi
_
O
O
phosphate
phosphate
+
Pi
hydrolysis can be altered so that it initially produces AMP and pyrophosphate (PPi), which is itself then hydrolyzed in solution in a subsequent
step (Figure 3–40). The whole
makes available a total ΔG of
ECB4process
e3.40/3.40
about –26 kcal/mole. The biosynthetic reaction involved in the synthesis
of nucleic acids (polynucleotides) is driven in this way (Figure 3–41).
ATP will make many appearances throughout the book as a molecule
that powers reactions in the cell. And in Chapters 13 and 14, we discuss
how the cell uses the energy from food to generate ATP. In the next chapter, we learn more about the proteins that make such reactions possible.
base
3
P
P
P O
sugar
base
1
OH
high-energy intermediate
P O
sugar
2 ATP
P O
P Pi
H2O
base
3
P
O
sugar
OH
nucleoside
monophosphate
2 ADP
sugar
OH
polynucleotide
chain containing
two nucleotides
2 Pi
products of
ATP hydrolysis
base
2
base
1
P O
sugar
P O
polynucleotide chain
containing three nucleotides
base
2
sugar
P O
base
3
sugar
OH
Figure 3–41 Synthesis of a polynucleotide,
RNA or DNA, is a multistep process
driven by ATP hydrolysis. In the first step,
a nucleoside monophosphate is activated
by the sequential transfer of the terminal
phosphate groups from two ATP molecules.
The high-energy intermediate formed—a
nucleoside triphosphate—exists free in
solution until it reacts with the growing
end of an RNA or a DNA chain with release
of pyrophosphate. Hydrolysis of the
pyrophosphate to inorganic phosphate
is highly favorable and helps to drive
the overall reaction in the direction of
polynucleotide synthesis.
116
Chapter 3
Energy, Catalysis, and Biosynthesis
Essential Concepts
•
Living organisms are able to exist because of a continual input of
energy. Part of this energy is used to carry out essential reactions
that support cell metabolism, growth, movement, and reproduction;
the remainder is lost in the form of heat.
•
The ultimate source of energy for most living organisms is the sun.
Plants, algae, and photosynthetic bacteria use solar energy to produce organic molecules from carbon dioxide. Animals obtain food by
eating plants or by eating animals that feed on plants.
•
Each of the many hundreds of chemical reactions that occur in a cell
is specifically catalyzed by an enzyme. Large numbers of different
enzymes work in sequence to form chains of reactions, called metabolic pathways, each performing a different function in the cell.
•
Catabolic reactions release energy by breaking down organic molecules, including foods, through oxidative pathways. Anabolic
reactions generate the many complex organic molecules needed by
the cell, and they require an energy input. In animal cells, both the
building blocks and the energy required for the anabolic reactions are
obtained through catabolic reactions.
•
Enzymes catalyze reactions by binding to particular substrate molecules in a way that lowers the activation energy required for making
and breaking specific covalent bonds.
•
The rate at which an enzyme catalyzes a reaction depends on how
rapidly it finds its substrates and how quickly the product forms and
then diffuses away. These rates vary widely from one enzyme to
another.
•
The only chemical reactions possible are those that increase the
total amount of disorder in the universe. The free-energy change for
a reaction, ΔG, measures this disorder, and it must be less than zero
for a reaction to proceed spontaneously.
•
The ΔG for a chemical reaction depends on the concentrations of the
reacting molecules, and it may be calculated from these concentrations if the equilibrium constant (K) of the reaction (or the standard
free-energy change, ΔG°, for the reactants) is known.
•
Equilibrium constants govern all of the associations (and dissociations) that occur between macromolecules and small molecules in
the cell. The larger the binding energy between two molecules, the
larger the equilibrium constant and the more likely that these molecules will be found bound to each other.
•
By creating a reaction pathway that couples an energetically favorable reaction to an energetically unfavorable one, enzymes can make
otherwise impossible chemical transformations occur.
•
A small set of activated carriers, particularly ATP, NADH, and NADPH,
plays a central part in these coupled reactions in cells. ATP carries
high-energy phosphate groups, whereas NADH and NADPH carry
high-energy electrons.
•
Food molecules provide the carbon skeletons for the formation of
macromolecules. The covalent bonds of these larger molecules are
produced by condensation reactions that are coupled to energetically favorable bond changes in activated carriers such as ATP and
NADPH.
Chapter 3 End-of-Chapter Questions
117
Key terms
acetyl CoA
free energy, G
activated carrier
free-energy change, ΔG
activation energy
hydrolysis
ADP, ATP
KM
anabolism
metabolism
biosynthesis
Michaelis constant (KM)
catabolismNAD+, NADH
catalysisNADP+, NADPH
catalyst
oxidation
condensation reaction
photosynthesis
coupled reaction
reduction
diffusion
respiration
entropy
standard free-energy change, ΔG°
enzyme
substrate
equilibrium
turnover number
equilibrium constant, K
Vmax
Questions
Question 3–10
Question 3–11
Which of the following statements are correct? Explain your
answers.
Consider a transition of X → Y. Assume that the only
difference between X and Y is the presence of three
hydrogen bonds in Y that are absent in X. What is the ratio
of X to Y when the reaction is in equilibrium? Approximate
your answer by using Table 3–1 (p. 98), with 1 kcal/mole
as the energy of each hydrogen bond. If Y instead has
six hydrogen bonds that distinguish it from X, how would
that change the ratio?
A.Some enzyme-catalyzed reactions cease completely if
their enzyme is absent.
B.High-energy electrons (such as those found in the
activated carriers NADH and NADPH) move faster around
the atomic nucleus.
C.Hydrolysis of ATP to AMP can provide about twice as
much energy as hydrolysis of ATP to ADP.
D.A partially oxidized carbon atom has a somewhat smaller
diameter than a more reduced one.
E.Some activated carrier molecules can transfer both
energy and a chemical group to a second molecule.
F. The rule that oxidations release energy, whereas
reductions require energy input, applies to all chemical
reactions, not just those that occur in living cells.
G. Cold-blooded animals have an energetic disadvantage
because they release less heat to the environment than
warm-blooded animals do. This slows their ability to make
ordered macromolecules.
H.Linking the reaction X → Y to a second, energetically
favorable reaction Y → Z will shift the equilibrium constant
of the first reaction.
Question 3–12
Protein A binds to protein B to form a complex, AB.
At equilibrium in a cell the concentrations of A, B, and AB
are all at 1 μM.
A.Referring to Figure 3–19, calculate the equilibrium
constant for the reaction A + B
AB.
B. What would the equilibrium constant be if A, B, and
AB were each present in equilibrium at the much lower
concentrations of 1 nM each?
C.How many extra hydrogen bonds would be needed to
hold A and B together at this lower concentration so that
a similar proportion of the molecules are found in the AB
complex? (Remember that each hydrogen bond contributes
about 1 kcal/mole.)
118
Chapter 3
Energy, Catalysis, and Biosynthesis
Question 3–13
Discuss the following statement: “Whether the ΔG for a
reaction is larger, smaller, or the same as ΔG° depends on
the concentration of the compounds that participate in the
reaction.”
Question 3–14
A.How many ATP molecules could maximally be generated
from one molecule of glucose, if the complete oxidation of
1 mole of glucose to CO2 and H2O yields 686 kcal of free
energy and the useful chemical energy available in the highenergy phosphate bond of 1 mole of ATP is 12 kcal?
B.As we will see in Chapter 14 (Table 14–1), respiration
produces 30 moles of ATP from 1 mole of glucose. Compare
this number with your answer in part (A). What is the overall
efficiency of ATP production from glucose?
C.If the cells of your body oxidize 1 mole of glucose, by
how much would the temperature of your body (assume
that your body consists of 75 kg of water) increase if the
heat were not dissipated into the environment? [Recall that
a kilocalorie (kcal) is defined as that amount of energy that
heats 1 kg of water by 1°C.]
D. What would the consequences be if the cells of your
body could convert the energy in food substances with
only 20% efficiency? Would your body—as it is presently
constructed—work just fine, overheat, or freeze?
E.A resting human hydrolyzes about 40 kg of ATP every
24 hours. The oxidation of how much glucose would
produce this amount of energy? (Hint: Look up the structure
of ATP in Figure 2–24 to calculate its molecular weight; the
atomic weights of H, C, N, O, and P are 1, 12, 14, 16, and
31, respectively.)
A.Do you suppose it might be safe for you to eat a
mushroom that bears this mutation? Base your answer on an
estimation of how much less poison the mutant mushroom
would produce, assuming the reaction is in equilibrium
and most of the energy stored in ATP is used to drive the
unfavorable reaction in nonmutant mushrooms.
B. Would your answer be different for another mutant
mushroom whose enzyme couples the reaction to ATP
hydrolysis but works 100 times more slowly?
Question 3–18
Consider the effects of two enzymes, A and B. Enzyme A
catalyzes the reaction
ATP + GDP
ADP + GTP
and enzyme B catalyzes the reaction
NADH + NADP+
NAD+ + NADPH
Discuss whether the enzymes would be beneficial or
detrimental to cells.
Question 3–19
Discuss the following statement: “Enzymes and heat are
alike in that both can speed up reactions that—although
thermodynamically feasible—do not occur at an appreciable
rate because they require a high activation energy. Diseases
that seem to benefit from the careful application of heat—in
the form of hot chicken soup, for example—are therefore
likely to be due to the insufficient function of an enzyme.”
Question 3–20
The curve shown in Figure 3–24 is described by the
Michaelis–Menten equation:
Question 3–15
rate (v) = Vmax [S]/([S] + KM)
A prominent scientist claims to have isolated mutant cells
that can convert 1 molecule of glucose into 57 molecules
of ATP. Should this discovery be celebrated, or do you
suppose that something might be wrong with it? Explain
your answer.
Can you convince yourself that the features qualitatively
described in the text are accurately represented by this
equation? In particular, how can the equation be simplified
when the substrate concentration [S] is in one of the
following ranges: (A) [S] is much smaller than the KM,
(B) [S] equals the KM, and (C) [S] is much larger than the KM?
Question 3–16
In a simple reaction A
A*, a molecule is interconvertible
between two forms that differ in standard free energy G° by
4.3 kcal/mole, with A* having the higher G°.
A. Use Table 3–1 (p. 98) to find how many more molecules
will be in state A* compared with state A at equilibrium.
B. If an enzyme lowered the activation energy of the
reaction by 2.8 kcal/mole, how would the ratio of A to A*
change?
Question 3–17
A reaction in a single-step biosynthetic pathway that
converts a metabolite into a particularly vicious poison
(metabolite
poison) in a mushroom is energetically
highly unfavorable. The reaction is normally driven by ATP
hydrolysis. Assume that a mutation in the enzyme that
catalyzes the reaction prevents it from utilizing ATP, but still
allows it to catalyze the reaction.
Question 3–21
The rate of a simple enzyme reaction is given by the
standard Michaelis–Menten equation:
rate = Vmax [S]/([S] + KM)
If the Vmax of an enzyme is 100 μmole/sec and the KM is
1 mM, at what substrate concentration is the rate
50 μmole/sec? Plot a graph of rate versus substrate (S)
concentration for [S] = 0 to 10 mM. Convert this to a plot of
1/rate versus 1/[S]. Why is the latter plot a straight line?
Question 3–22
Select the correct options in the following and explain your
choices. If [S] is much smaller than KM, the active site of the
enzyme is mostly occupied/unoccupied. If [S] is very much
greater than KM, the reaction rate is limited by the enzyme/
substrate concentration.
Chapter 3 End-of-Chapter Questions
Question 3–23
A. The reaction rates of the reaction S → P catalyzed by
enzyme E were determined under conditions such that only
very little product was formed. The following data were
measured:
SubstrateReaction rate
concentration (μM)
(μmole/min)
0.08
0.15
0.12
0.21
0.54
0.7
1.23
1.1
1.82
1.3
2.72
1.5
4.94
1.7
10.00
1.8
Plot the above data as a graph. Use this graph to estimate
the KM and the Vmax for this enzyme.
B. Recall from the How We Know essay (pp. 104–106) that
to determine these values more precisely, a trick is generally
used in which the Michaelis–Menten equation is transformed
so that it is possible to plot the data as a straight line.
A simple rearrangement yields
1/rate = (KM/Vmax) (1/[S]) + 1/Vmax
which is an equation of the form y = ax + b. Calculate
1/rate and 1/[S] for the data given in part (A) and then plot
1/rate versus 1/[S] as a new graph. Determine KM and Vmax
from the intercept of the line with the axis, where 1/[S] = 0,
combined with the slope of the line. Do your results agree
with the estimates made from the first graph of the raw
data?
C.It is stated in part (A) that only very little product
was formed under the reaction conditions. Why is this
important?
D.Assume the enzyme is regulated such that upon
phosphorylation its KM increases by a factor of 3 without
changing its Vmax. Is this an activation or inhibition? Plot the
data you would expect for the phosphorylated enzyme in
both the graph for (A) and the graph for (B).
119
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chapter FOUR
4
Protein Structure and Function
When we look at a cell in a microscope or analyze its electrical or biochemical activity, we are, in essence, observing the handiwork of proteins.
Proteins are the main building blocks from which cells are assembled,
and they constitute most of the cell’s dry mass. In addition to providing the cell with shape and structure, proteins also execute nearly all its
myriad functions. Enzymes promote intracellular chemical reactions by
providing intricate molecular surfaces, contoured with particular bumps
and crevices that can cradle or exclude specific molecules. Proteins
embedded in the plasma membrane form the channels and pumps that
control the passage of nutrients and other small molecules into and out
of the cell. Other proteins carry messages from one cell to another, or
act as signal integrators that relay information from the plasma membrane to the nucleus of individual cells. Some proteins act as motors that
propel organelles through the cytoplasm, and others function as components of tiny molecular machines with precisely calibrated moving parts.
Specialized proteins also act as antibodies, toxins, hormones, antifreeze
molecules, elastic fibers, or luminescence generators. Before we can
hope to understand how genes work, how muscles contract, how nerves
conduct electricity, how embryos develop, or how our bodies function,
we must understand proteins.
The multiplicity of functions carried out by proteins (Panel 4–1, p. 122)
arises from the huge number of different shapes they adopt. We therefore
begin our description of these remarkable macromolecules by discussing
their three-dimensional structures and the properties that these structures confer. We next look at how proteins work: how enzymes catalyze
chemical reactions, how some proteins act as molecular switches, and
how others generate orderly movement. We then examine how cells
The Shape and Structure
of Proteins
HOW PROTEINS WORK
HOW PROTEINS ARE
CONTROLLED
HOW PROTEINS ARE STUDIED
122
Panel 4–1
A FEW EXAMPLES OF SOME GENERAL PROTEIN FUNCTIONS
ENZYMES
function: Catalyze covalent bond breakage
or formation.
STRUCTURAL PROTEINS
TRANSPORT PROTEINS
function: Provide mechanical support to
cells and tissues.
function: Carry small molecules or ions.
examples: Outside cells, collagen and elastin
are common constituents of extracellular
matrix and form fibers in tendons and
ligaments. Inside cells, tubulin forms long, stiff
microtubules, and actin forms filaments that
underlie and support the plasma membrane;
keratin forms fibers that reinforce epithelial
cells and is the major protein in hair and horn.
examples: In the bloodstream, serum albumin
carries lipids, hemoglobin carries oxygen, and
transferrin carries iron. Many proteins embedded
in cell membranes transport ions or small
molecules across the membrane. For example, the
bacterial protein bacteriorhodopsin is a
light-activated proton pump that transports H+
ions out of the cell; glucose carriers shuttle
glucose into and out of cells; and a Ca2+ pump
clears Ca2+ from a muscle cell’s cytosol after the
ions have triggered a contraction.
MOTOR PROTEINS
STORAGE PROTEINS
SIGNAL PROTEINS
function: Generate movement in cells and
tissues.
function: Store amino acids or ions.
function: Carry extracellular signals from
cell to cell.
examples: Living cells contain thousands of
different enzymes, each of which catalyzes
(speeds up) one particular reaction. Examples
include: tryptophan synthetase—makes the
amino acid tryptophan; pepsin—degrades
dietary proteins in the stomach; ribulose
bisphosphate carboxylase—helps convert
carbon dioxide into sugars in plants; DNA
polymerase—copies DNA; protein
kinase—adds a phosphate group to a
protein molecule.
examples: Myosin in skeletal muscle cells
provides the motive force for humans to
move; kinesin interacts with microtubules to
move organelles around the cell; dynein
enables eukaryotic cilia and flagella to beat.
examples: Iron is stored in the liver by
binding to the small protein ferritin;
ovalbumin in egg white is used as a source
of amino acids for the developing bird
embryo; casein in milk is a source of amino
acids for baby mammals.
examples: Many of the hormones and growth
factors that coordinate physiological functions
in animals are proteins; insulin, for example, is
a small protein that controls glucose levels in
the blood; netrin attracts growing nerve cell
axons to specific locations in the developing
spinal cord; nerve growth factor (NGF)
stimulates some types of nerve cells to grow
axons; epidermal growth factor (EGF)
stimulates the growth and division of
epithelial cells.
RECEPTOR PROTEINS
GENE REGULATORY PROTEINS
SPECIAL-PURPOSE PROTEINS
function: Detect signals and transmit them
to the cell's response machinery.
examples: Rhodopsin in the retina detects
light; the acetylcholine receptor in the
membrane of a muscle cell is activated by
acetylcholine released from a nerve ending;
the insulin receptor allows a cell to respond to
the hormone insulin by taking up glucose; the
adrenergic receptor on heart muscle increases
the rate of the heartbeat when it binds to
adrenaline.
function: Bind to DNA to switch genes on
or off.
examples: The lactose repressor in bacteria
silences the genes for the enzymes that
degrade the sugar lactose; many different
homeodomain proteins act as genetic
switches to control development in
multicellular organisms, including humans.
function: Highly variable.
examples: Organisms make many proteins with
highly specialized properties. These molecules
illustrate the amazing range of functions that
proteins can perform. The antifreeze proteins of
Arctic and Antarctic fishes protect their blood
against freezing; green fluorescent protein from
jellyfish emits a green light; monellin, a protein
found in an African plant, has an intensely sweet
taste; mussels and other marine organisms secrete
glue proteins that attach them firmly to rocks,
even when immersed in seawater.
The Shape and Structure of Proteins
123
control the activity and location of the proteins they contain. Finally, we
present a brief description of the techniques that biologists use to work
with proteins, including methods for purifying them—from tissues or cultured cells—and for determining their structures.
The Shape and Structure of Proteins
From a chemical point of view, proteins are by far the most structurally complex and functionally sophisticated molecules known. This is
perhaps not surprising, considering that the structure and activity of
each protein has been developed and fine-tuned over billions of years
of evolution. We start by considering how the position of each amino
acid in the long string of amino acids that forms a protein determines its
three-dimensional shape, which is stabilized by noncovalent interactions
between different parts of the molecule. Understanding the structure of a
protein at the atomic level allows us to see how the precise shape of the
protein determines its function.
The Shape of a Protein Is Specified by Its Amino Acid
Sequence
Proteins, as you may recall from Chapter 2, are assembled mainly from
a set of 20 different amino acids, each with different chemical properties. A protein molecule is made from a long chain of these amino acids,
held together by covalent peptide bonds (Figure 4–1). Proteins are therefore referred to as polypeptides, and their amino acid chains are called
polypeptide chains. In each type of protein, the amino acids are present
in a unique order, called the amino acid sequence, which is exactly the
same from one molecule of that protein to the next. One molecule of
human insulin, for example, has the same amino acid sequence as every
other molecule of human insulin. Many thousands of different proteins
have been identified, each with its own distinct amino acid sequence.
amino
group
carboxyl
group
+
+
–
–
glycine
alanine
PEPTIDE BOND
FORMATION WITH
REMOVAL OF WATER
water
+
–
peptide bond in glycylalanine
Figure 4–1 Amino acids are linked
together by peptide bonds. A covalent
peptide bond forms when the carbon atom
of the carboxyl group of one amino acid
(such as glycine) shares electrons with the
nitrogen atom (blue) from the amino group
of a second amino acid (such as alanine).
Because a molecule of water is eliminated,
peptide bond formation is classified as a
condensation reaction (see Figure 2–29).
In this diagram, carbon atoms are gray,
nitrogen blue, oxygen red, and
hydrogen white.
124
Chapter 4
Protein Structure and Function
Figure 4–2 A protein is made
of amino acids linked together
into a polypeptide chain. The
amino acids are linked by peptide
bonds (see Figure 4–1) to form
a polypeptide backbone of
repeating structure (gray boxes),
from which the side chain of each
amino acid projects. The character
and sequence of the chemically
distinct side chains—for example,
nonpolar (green), polar uncharged
(yellow), and negative (blue) side
chains—give each protein its
distinct, individual properties.
A small polypeptide of just four
amino acids is shown here. Proteins
are typically made up of chains of
several hundred amino acids, whose
sequence is always presented
starting with the N-terminus reading
from left to right.
OH
O
O
C
polypeptide backbone
H
H
O
+
amino terminus
H N
(N-terminus)
C
C
H
CH2
CH2
side chains
CH2
N
C
C
H
H
O
Methionine
(Met)
H
O
N
C
C
O
N
C
H
H
CH2
peptide
bonds
C
carboxyl terminus
(C-terminus)
O
peptide bond
CH
H3C
S
CH3
H
CH2
CH3
side chains
Aspartic acid
(Asp)
Leucine
(Leu)
Tyrosine
(Tyr)
Each polypeptide chain consists of a backbone that is adorned with a
variety of chemical side chains. This polypeptide backbone is formed
from a repeating sequence of the core atoms (–N–C–C–) found in every
amino acid (see Figure 4–1). Because the two ends of each amino acid
are chemically different—one sports an amino group (NH3+, also written
NH2) and the other a ECB4
carboxyl
group (COO–, also written COOH)—each
m3.01/4.02
polypeptide chain has a directionality: the end carrying the amino group
is called the amino terminus, or N-terminus, and the end carrying the
free carboxyl group is the carboxyl terminus, or C-terminus.
Projecting from the polypeptide backbone are the amino acid side
chains—the part of the amino acid that is not involved in forming peptide bonds (Figure 4–2). The side chains give each amino acid its unique
properties: some are nonpolar and hydrophobic (“water-fearing”), some
are negatively or positively charged, some can be chemically reactive,
and so on. The atomic formula for each of the 20 amino acids in proteins
is presented in Panel 2–5 (pp. 74–75), and a brief list of the 20 common
amino acids, with their abbreviations, is provided in Figure 4–3.
AMINO ACID
Aspartic acid
Glutamic acid
Arginine
Lysine
Histidine
Asparagine
Glutamine
Serine
Threonine
Tyrosine
Asp
Glu
Arg
Lys
His
Asn
Gln
Ser
Thr
Tyr
SIDE CHAIN
D
E
R
K
H
N
Q
S
T
Y
AMINO ACID
negatively charged
negatively charged
positively charged
positively charged
positively charged
uncharged polar
uncharged polar
uncharged polar
uncharged polar
uncharged polar
Alanine
Glycine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan
Cysteine
POLAR AMINO ACIDS
Ala
Gly
Val
Leu
Ile
Pro
Phe
Met
Trp
Cys
SIDE CHAIN
A
G
V
L
I
P
F
M
W
C
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
NONPOLAR AMINO ACIDS
Figure 4–3 Twenty different amino acids are commonly found in proteins. Both three-letter and one-letter abbreviations are given,
as well as the character of the side chain. There are equal numbers of polar (hydrophilic) and nonpolar (hydrophobic) side chains, and
half of the polar side chains carry a positive or negative charge.
ECB4 m3.02/4.03
The Shape and Structure of Proteins
125
glutamic acid
N
H
H
O
C
C
electrostatic
attractions
CH2
+
R
CH2
C
O
O
H
H
H
N
+
C
hydrogen bond
O
C
CH2
CH2
van der Waals attractions
CH2
C
C
O
H
lysine
H
N
H C
CH3 CH3
valine
CH3 CH3
C
C
H
N
N
H
C
R
O
O
C H
HN
CH3
C
N
C
H
C
H
O
C N C
H
H
O
H
O
H
H
C
R
CH2
C
H
valine
alanine
Long polypeptide chains are very flexible, as many of the peptide bonds
that link the carbon atoms in the polypeptide backbone allow free rotation of the atoms they join. Thus, proteins can in principle fold in an
enormous number of ways. The shape of each of these folded chains,
however, is constrained by many sets of weak noncovalent bonds that
MBoC6 m3.04/4.04
form within proteins. These bonds involve atoms in the polypeptide
backbone, as well as atoms in the amino acid side chains. The noncovalent bonds that help proteins fold up and maintain their shape include
hydrogen bonds, electrostatic attractions, and van der Waals attractions,
which are described in Chapter 2 (see Panel 2–7, pp. 78–79). Because a
noncovalent bond is much weaker than a covalent bond, it takes many
noncovalent bonds to hold two regions of a polypeptide chain tightly
together. The stability of each folded shape is largely influenced by the
combined strength of large numbers of noncovalent bonds (Figure 4–4).
A fourth weak force, hydrophobic interaction, also has a central role in
determining the shape of a protein. In an aqueous environment, hydrophobic molecules, including the nonpolar side chains of particular amino
acids, tend to be forced together to minimize their disruptive effect on
the hydrogen-bonded network of the surrounding water molecules (see
Panel 2–2, pp. 68–69). Therefore, an important factor governing the folding of any protein is the distribution of its polar and nonpolar amino
acids. The nonpolar (hydrophobic) side chains—which belong to amino
acids such as phenylalanine, leucine, valine, and tryptophan (see Figure
4–3)—tend to cluster in the interior of the folded protein (just as hydrophobic oil droplets coalesce to form one large drop). Tucked away inside
the folded protein, hydrophobic side chains can avoid contact with the
aqueous cytosol that surrounds them inside a cell. In contrast, polar side
chains—such as those belonging to arginine, glutamine, and histidine—
tend to arrange themselves near the outside of the folded protein, where
they can form hydrogen bonds with water and with other polar molecules (Figure 4–5). When polar amino acids are buried within the protein,
they are usually hydrogen-bonded to other polar amino acids or to the
polypeptide backbone (Figure 4–6).
Figure 4–4 Three types of noncovalent
bonds help proteins fold. Although a
single one of any of these bonds is quite
weak, many of them together can create a
strong bonding arrangement that stabilizes
a particular three-dimensional structure,
as in the small polypeptide shown in
the center. R is often used as a general
designation for an amino acid side chain.
Protein folding is also aided by hydrophobic
forces, as shown in Figure 4–5.
126
Chapter 4
Protein Structure and Function
Figure 4–5 Hydrophobic forces help
proteins fold into compact conformations.
Polar amino acid side chains tend to be
displayed on the outside of the folded
protein, where they can interact with water;
the nonpolar amino acid side chains are
buried on the inside to form a highly packed
hydrophobic core of atoms that are hidden
from water.
nonpolar side chains
polar side chains
unfolded polypeptide
hydrophobic
core region
contains
nonpolar
side chains
hydrogen bonds can
form between water
and the polar side
chains on the outside
of the protein
folded conformation in aqueous environment
Proteins Fold into a Conformation of Lowest Energy
Each type of protein has a particular three-dimensional structure, which
is determined by the order of the amino acids in its polypeptide chain.
The final folded structure, or conformation, adopted by any polypeptide
chain is determined by energetic considerations: a protein generally folds
ECB4 e4.05/4.05
into the shape in which its free energy
(G) is minimized. The folding process is thus energetically favorable, as it releases heat and increases the
disorder of the universe (see Panel 3–1, pp. 96–97).
Protein folding has been studied in the laboratory using highly purified
proteins. A protein can be unfolded, or denatured, by treatment with solvents that disrupt the noncovalent interactions holding the folded chain
together. This treatment converts the protein into a flexible polypeptide
chain that has lost its natural shape. Under the right conditions, when the
42
Figure 4–6 Hydrogen bonds within a
protein molecule help stabilize its folded
shape. Large numbers of hydrogen bonds
form between adjacent regions of the
folded polypeptide chain. The structure
shown is a portion of the enzyme lysozyme.
Hydrogen bonds between backbone
atoms are shown in red ; those between
the backbone and a side chain are shown
in yellow ; and those between atoms of two
side chains are shown in blue. Note that
the same amino acid side chain can make
multiple hydrogen bonds (red arrow). The
atoms are colored as in Figure 4–1, although
the hydrogen atoms are not shown. (After
C.K. Mathews, K.E. van Holde, and
K.G. Ahern, Biochemistry, 3rd ed. San
Francisco: Benjamin Cummings, 2000.)
63
backbone to backbone
backbone to side chain
side chain to side chain
hydrogen bond between
atoms of two peptide
bonds
hydrogen bond between
atoms of a peptide bond
and an amino acid side chain
hydrogen bond between
two amino acid side
chains
The Shape and Structure of Proteins
EXPOSE TO A HIGH
CONCENTRATION
OF UREA
REMOVE
UREA
purified protein
isolated from cells
protein refolds into its
original conformation
Figure 4–7 Denatured proteins can
often recover their natural shapes. This
type of experiment demonstrates that the
conformation of a protein is determined
solely by its amino acid sequence.
Renaturation requires the correct conditions
and works best for small proteins.
denatured protein
denaturing solvent is removed, the protein often refolds spontaneously
into its original conformation—a process called renaturation (Figure 4–7).
The fact that a denatured protein can, on its own, refold into the correct conformation indicates that all the information necessary to specify
the three-dimensional shape of a protein is contained in its amino acid
sequence.
ECB4 e4.07/4.07
Each protein normally folds into a single stable conformation. This conformation, however, often changes slightly when the protein interacts
with other molecules in the cell. This change in shape is crucial to the
function of the protein, as we discuss later.
When proteins fold incorrectly, they sometimes form aggregates that can
damage cells and even whole tissues. Misfolded proteins are thought
to contribute to a number of neurodegenerative disorders, such as
Alzheimer’s disease and Huntington’s disease. Some infectious neurodegenerative diseases—including scrapie in sheep, bovine spongiform
encephalopathy (BSE, or “mad cow” disease) in cattle, and Creutzfeldt–
Jakob disease (CJD) in humans—are caused by misfolded proteins called
prions. The misfolded prion form of a protein can convert the properly
folded version of the protein in an infected brain into the abnormal conformation. This allows the misfolded prions, which tend to form aggregates,
to spread rapidly from cell to cell, eventually causing the death of the
affected animal or human (Figure 4–8). Prions are considered “infectious”
because they can also spread from an affected individual to a normal
individual via contaminated food, blood, or surgical instruments, for
example.
Although a protein chain can fold into its correct conformation without
outside help, protein folding in a living cell is generally assisted by special proteins called chaperone proteins. Some of these chaperones bind
to partly folded chains and help them to fold along the most energetically favorable pathway (Figure 4–9). Others form “isolation chambers”
in which single polypeptide chains can fold without the risk of forming
aggregates in the crowded conditions of the cytoplasm (Figure 4–10). In
either case, the final three-dimensional shape of the protein is still specified by its amino acid sequence; chaperones merely make the folding
process more efficient and reliable.
Proteins Come in a Wide Variety of Complicated Shapes
Question 4–1
Urea used in the experiment shown
in Figure 4–7 is a molecule that
disrupts the hydrogen-bonded
network of water molecules. Why
might high concentrations of urea
unfold proteins? The structure of
urea is shown here.
O
C
H2N
NH2
(A) normal protein can, on occasion, adopt
an abnormal, misfolded prion form
ECB4 Q4.01/Q4.01
normal
protein
abnormal prion form
of protein
(B) the prion form of the protein can bind
to the normal form, inducing conversion
to the abnormal conformation
binding
heterodimer
conversion of normal
protein to abnormal
prion form
Proteins are the most structurally diverse macromolecules in the cell.
Although they range in size from about 30 amino acids to more than
Figure 4–8 Prion diseases are caused by proteins whose misfolding
is infectious. (A) The protein undergoes a rare conformational change
to give an abnormally folded prion form. (B) The abnormal form causes
the conversion of normal proteins in the host’s brain into a misfolded
prion form. (C) The prions aggregate into amyloid fibrils, which disrupt
brain cell function, causing a neurodegenerative disorder, such as
“mad cow” disease (see also Figure 4–18).
127
(C) abnormal prion proteins propagate
and aggregate to form amyloid fibrils
amyloid fibril
128
Chapter 4
Protein Structure and Function
Figure 4–9 Chaperone proteins can
guide the folding of a newly synthesized
polypeptide chain. The chaperones bind to
newly synthesized or partially folded chains
and helping them to fold along the most
energetically favorable pathway.
Association of these chaperones with the
target protein requires an input of energy
from ATP hydrolysis.
newly synthesized,
partially folded protein
chaperone
proteins
incorrectly folded
protein
correctly folded
protein
10,000, the vast majority are between 50 and 2000 amino acids long.
Proteins can be globular or fibrous, and they can form filaments, sheets,
rings, or spheres (Figure 4–11). We will encounter many of these structures later in this chapter and throughout the book.
ECB4 n4.100/4.09
To date, the structures of about 100,000 different proteins have been
determined. We discuss how scientists unravel these structures later in
the chapter. Most proteins have a three-dimensional conformation so
intricate and irregular that their structure would require an entire chapter to describe in detail. But we can get some sense of the intricacies of
polypeptide structure by looking at the conformation of a relatively small
protein, such as the bacterial transport protein HPr.
This small protein is only 88 amino acids long, and it serves as a carrier protein that facilitates the transport of sugar into bacterial cells. In
Figure 4–12, we present HPr’s three-dimensional structure in four different ways, each of which emphasizes different features of the protein.
The backbone model (Figure 4–12A) shows the overall organization of
the polypeptide chain and provides a straightforward way to compare the
structures of related proteins. The ribbon model (Figure 4–12B) shows the
polypeptide backbone in a way that emphasizes its various folds, which
we describe in detail shortly. The wire model (Figure 4–12C) includes the
positions of all the amino acid side chains; this view is especially useful
newly synthesized,
partially folded proteins
chaperone
protein
chamber
cap
one polypeptide
chain is sequestered
by the chaperone
isolated
polypeptide
chain folds
correctly
correctly folded
protein is released
when cap
dissociates
Figure 4–10 Other chaperone proteins act as isolation chambers that help a
polypeptide fold. In this case, the barrel of the chaperone provides an enclosed
chamber in which a newly synthesized polypeptide chain can fold without the risk of
aggregating with other polypeptides in the crowded conditions of the cytoplasm.
ECB4 n4.101/4.10
This system also requires an input of energy from ATP hydrolysis, mainly for the
association and subsequent dissociation of the cap that closes off the chamber.
The Shape and Structure of Proteins
carrier
protein HPr
lysozyme
catalase
myoglobin
hemoglobin
DNA
deoxyribonuclease
collagen
porin
cytochrome c
chymotrypsin
calmodulin
aspartate
transcarbamoylase
insulin
alcohol
dehydrogenase
5 nm
Figure 4–11 Proteins come in a variety of shapes and sizes. Each folded polypeptide is shown as a space-filling model, represented
at the same scale. In the top-left corner is HPr, the small protein featured in detail in Figure 4–12. For comparison we also show a
portion of a DNA molecule (gray) bound to the protein
deoxyribonuclease. (After David S. Goodsell, Our Molecular Nature. New York:
ECB4 e4.09/4.11
Springer-Verlag, 1996. With permission from Springer Science and Business Media.)
129
130
Chapter 4
Protein Structure and Function
(A) backbone model
Figure 4–12 Protein conformation can be represented in a variety
of ways. Shown here is the structure of the small bacterial transport
protein HPr. The images are colored to make it easier to trace the path
of the polypeptide chain. In these models, the region of polypeptide
chain carrying the protein’s N-terminus is purple and that near its
C-terminus is red.
for predicting which amino acids might be involved in the protein’s activity. Finally, the space-filling model (Figure 4–12D) provides a contour map
of the protein surface, which reveals which amino acids are exposed on
the surface and shows how the protein might look to a small molecule
such as water or to another macromolecule in the cell.
(B) ribbon model
The structures of larger proteins—or of multiprotein complexes—are
even more complex. To visualize such detailed and complicated structures, scientists have developed various graphical and computer-based
tools that generate a variety of images of a protein, only some of which
are depicted in Figure 4–12. These images can be displayed on a computer screen and readily rotated and magnified to view all aspects of the
structure (Movie 4.1).
When the three-dimensional structures of many different protein
molecules are compared, it becomes clear that, although the overall conformation of each protein is unique, some regular folding patterns can be
detected, as we discuss next.
(C) wire model
The α Helix and the β Sheet Are Common Folding Patterns
More than 60 years ago, scientists studying hair and silk discovered two
common folding patterns present in many different proteins. The first to
be discovered, called the α helix, was found in the protein α-keratin, which
is abundant in skin and its derivatives—such as hair, nails, and horns.
Within a year of the discovery of the α helix, a second folded structure,
called a β sheet, was found in the protein fibroin, the major constituent
of silk. (Biologists often use Greek letters to name their discoveries, with
the first example receiving the designation α, the second β, and so on.)
(D) space-filling model
These two folding patterns are particularly common because they result
from hydrogen bonds that form between the N–H and C=O groups in
the polypeptide backbone (see Figure 4–6). Because the amino acid side
chains are not involved in forming these hydrogen bonds, α helices and β
sheets can be generated by many different amino acid sequences. In each
case, the protein chain adopts a regular, repeating form. These structural
features, and the shorthand cartoon symbols that are often used to represent them in models of protein structures, are presented in Figure 4–13.
Helices Form Readily in Biological Structures
The abundance of helices in proteins is, in a way, not surprising. A helix
is a regular structure that resembles a spiral staircase. It is generated
simply by placing many similar subunits next to one another, each in
the same strictly repeated relationship to the one before. Because it is
very rare for subunits to join up in a straight line, this arrangement will
generally result in a helix (Figure 4–14). Depending on the twist of the
staircase, a helix is said to be either right-handed or left-handed (Figure
4–14E). Handedness is not affected by turning the helix upside down, but
it is reversed if the helix is reflected in a mirror.
An α helix is generated when a single polypeptide chain turns around
itself to form a structurally rigid cylinder. A hydrogen bond is made
between every fourth amino acid, linking the C=O of one peptide bond to
The Shape and Structure of Proteins
Figure 4–13 Polypeptide chains often fold
into one of two orderly repeating forms
known as an α helix and a β sheet.
(A–C) In an α helix, the N–H of every
peptide bond is hydrogen-bonded to
the C=O of a neighboring peptide bond
located four amino acids away in the same
chain. (D–F) In a β sheet, several segments
(strands) of an individual polypeptide chain
are held together by hydrogen-bonding
between peptide bonds in adjacent strands.
The amino acid side chains in each strand
project alternately above and below
the plane of the sheet. In the example
shown, the adjacent chains run in opposite
directions, forming an antiparallel β sheet.
(A) and (D) show all of the atoms in the
polypeptide backbone, but the amino acid
side chains are denoted by R. (B) and (E)
show only the carbon (black and gray) and
nitrogen (blue) backbone atoms, while (C)
and (F) display the cartoon symbols that
are used to represent the α helix and the
β sheet in ribbon models of proteins (see
Figure 4–12B).
α helix
amino acid
side chain
R
R
R
oxygen
R
0.54 nm
hydrogen bond
R
carbon
hydrogen
R
R
carbon
nitrogen
R
nitrogen
R
(B)
(A)
(C)
β sheet
amino acid
side chain
hydrogen bond
hydrogen
R
carbon
R
R
nitrogen
R
0.7 nm
carbon
R
R
peptide
bond
R
R
oxygen
R
(D)
R
R
R
R
R
R
(E)
131
(F)
the N–H of another (see Figure 4–13A). This gives rise to a regular righthanded helix with a complete turn every 3.6 amino acids (Movie 4.2).
especially
abundant in proteins that are
Short regions of α helix areECB4
m3.07/4.13
embedded in cell membranes, such as transport proteins and receptors.
We will see in Chapter 11 that those portions of a transmembrane protein that cross the lipid bilayer usually form an α helix that is composed
largely of amino acids with nonpolar side chains. The polypeptide backbone, which is hydrophilic, is hydrogen-bonded to itself in the α helix,
and it is shielded from the hydrophobic lipid environment of the membrane by its protruding nonpolar side chains (Figure 4–15).
Sometimes two (or three) α helices will wrap around one another to
form a particularly stable structure known as a coiled-coil. This structure forms when the α helices have most of their nonpolar (hydrophobic)
side chains on one side, so that they can twist around each other with
Question 4–2
Remembering that the amino
acid side chains projecting from
each polypeptide backbone in a
β sheet point alternately above
and below the plane of the sheet
(see Figure 4–13D), consider
the following protein sequence:
Leu-Lys-Val-Asp-Ile-Ser-Leu-ArgLeu-Lys-Ile-Arg-Phe-Glu. Do you
find anything remarkable about the
arrangement of the amino acids in
this sequence when incorporated
into a β sheet? Can you make any
predictions as to how the β sheet
might be arranged in a protein?
(Hint: consult the properties of the
amino acids listed in Figure 4–3.)
132
Chapter 4
Protein Structure and Function
Figure 4–14 The helix is a common,
regular, biological structure. A helix will
form when a series of similar subunits
bind to each other in a regular way. At
the bottom, the interaction between two
subunits is shown; behind them are the
helices that result. These helices have two
(A), three (B), or six (C and D) subunits per
helical turn. At the top, the arrangement
of subunits has been photographed from
directly above the helix. Note that the
helix in (D) has a wider path than that in
(C), but the same number of subunits per
turn. (E) A helix can be either right-handed
or left-handed. As a reference, it is useful
to remember that standard metal screws,
which advance when turned clockwise, are
right-handed. So to judge the handedness
of a helix, imagine screwing it into a wall.
Note that a helix preserves the same
handedness when it is turned upside down.
lefthanded
(A)
(B)
(C)
(D)
righthanded
(E)
these side chains facing inward—minimizing their contact with the aqueous cytosol (Figure 4–16). Long, rodlike coiled-coils form the structural
framework for many elongated
proteins. Examples include α-keratin,
ECB4 m3.26/4.14
which forms the intracellular fibers that reinforce the outer layer of the
skin, and myosin, the motor protein responsible for muscle contraction
(discussed in Chapter 17).
hydrophobic amino acid
side chain
hydrogen bond
β Sheets Form Rigid Structures at the Core of Many
Proteins
A β sheet is made when hydrogen bonds form between segments of a
polypeptide chain that lie side by side (see Figure 4–13D). When the neighboring segments run in the same orientation (say, from the N-terminus to
the C-terminus), the structure is a parallel β sheet; when they run in opposite directions, the structure is an antiparallel β sheet (Figure 4–17). Both
types of β sheet produce a very rigid, pleated structure, and they form the
core of many proteins. Even the small bacterial protein HPr (see Figure
4–12) contains several β sheets.
β sheets have remarkable properties. They give silk fibers their extraor-
phospholipid
in lipid bilayer
α helix
Figure 4–15 Many membrane-bound
proteins cross the lipid bilayer as an
α helix. The hydrophobic side chains
of the amino acids forming the α helix
contact the hydrophobic hydrocarbon
tails of the phospholipid molecules, while
the hydrophilic parts of the polypeptide
backbone form hydrogen bonds with one
another in the interior of the helix. About
20 amino acids are required to span a
membrane in this way. Note that, despite
the appearance of a space along the interior
of the helix in this schematic diagram, the
helix is not a channel: no ions or small
molecules can pass through it.
ECB4 e4.12/4.15
dinary tensile strength. They also permit the formation of amyloid
fibers—insoluble protein aggregates that include those associated with
neurodegenerative disorders, such as Alzheimer’s disease and prion diseases (see Figure 4–8). These structures, formed from abnormally folded
proteins, are stabilized by β sheets that stack together tightly, with their
amino acid side chains interdigitated like the teeth of a zipper (Figure
4–18). Although we tend to associate amyloid fibers with disease, many
organisms take advantage of these stable structures to perform novel
tasks. Infectious bacteria, for example, can use amyloid fibers to help
form the biofilms that allow them to colonize host tissues. Other types of
filamentous bacteria use amyloid fibers to extend filaments into the air,
enabling the bacteria to disperse their spores far and wide.
Proteins Have Several Levels of Organization
A protein’s structure does not end with α helices and β sheets; there are
additional levels of organization. These levels are not independent but
are built one upon the next to establish the three-dimensional structure
of the entire protein. A protein’s structure begins with its amino acid
sequence, which is thus considered its primary structure. The next
level of organization includes the α helices and β sheets that form within
The Shape and Structure of Proteins
Figure 4–16 Intertwined α helices can
form a stiff coiled-coil. In (A), a single α
helix is shown, with successive amino acid
side chains labeled in a sevenfold repeating
sequence “abcdefg.” Amino acids “a” and
“d” in such a sequence lie close together
on the cylinder surface, forming a stripe
(shaded in green) that winds slowly around
the α helix. Proteins that form coiled-coils
typically have nonpolar amino acids at
positions “a” and “d.” Consequently, as
shown in (B), the two α helices can wrap
around each other, with the nonpolar side
chains of one α helix interacting with the
nonpolar side chains of the other, while the
more hydrophilic amino acid side chains
(shaded in red ) are left exposed to the
aqueous environment. (C) A portion of
the atomic structure of a coiled-coil made
of two α helices, as determined by X-ray
crystallography. In this structure, atoms that
form the backbone of the helices are shown
in red; the interacting, nonpolar side chains
are green, and the remaining side chains
are gray. Coiled-coils can also form from
three α helices (Movie 4.3).
a NH 2
e
d
a
e
d
a
g
stripe of
hydrophobic
“a” and “d”
amino acids
d
a
g
11 nm
d
c
g
a
d
c
helices wrap around each other to minimize
exposure of hydrophobic amino acid
side chains to aqueous environment
COOH
0.5 nm
(A)
(B)
133
(C)
certain segments of the polypeptide chain; these folds are elements of
the protein’s secondary structure. The full, three-dimensional conformation formed by an entire polypeptide chain—including the α helices,
β sheets, random coils, and any other loops and folds that form
between the N- and C-termini—is sometimes referred to as the tertiary
structure. Finally, if the protein molecule is formed as a complex of more
than one polypeptide chain, then the complete structure is designated its
quaternary structure. ECB4 m3.09/4.16
Studies of the conformation, function, and evolution of proteins have
also revealed the importance of a level of organization distinct from
the four just described. This organizational unit is the protein domain,
which is defined as any segment of a polypeptide chain that can fold
independently into a compact, stable structure. A protein domain usually
contains between 40 and 350 amino acids—folded into α helices and β
sheets and other elements of secondary structure—and it is the modular unit from which many larger proteins are constructed (Figure 4–19).
The different domains of a protein are often associated with different
functions. For example, the bacterial catabolite activator protein (CAP),
illustrated in Figure 4–19, has two domains: the small domain binds to
DNA, while the large domain binds cyclic AMP, a small intracellular signaling molecule. When the large domain binds cyclic AMP, it causes a
conformational change in the protein that enables the small domain to
bind to a specific DNA sequence and thereby promote the expression of
an adjacent gene. To provide a sense of the many different domain structures observed in proteins, ribbon models of three different domains are
shown in Figure 4–20.
Figure 4–17 β sheets come in two varieties. (A) Antiparallel β sheet
(see also Figure 4–13D). (B) Parallel β sheet. Both of these structures
are common in proteins. By convention, the arrows point toward the
C-terminus of the polypeptide chain (Movie 4.4).
(A)
(B)
134
Chapter 4
Protein Structure and Function
Many Proteins Also Contain Unstructured Regions
Small protein molecules, such as the oxygen-carrying muscle protein
myoglobin, contain only a single domain (see Figure 4–11). Larger proteins can contain as many as several dozen domains, which are usually
connected by relatively unstructured lengths of polypeptide chain. Such
regions of polypeptide chain lacking any definite structure, which continually bend and flex due to thermal buffeting, are abundant in cells. These
intrinsically disordered sequences are often found as short stretches
linking domains in otherwise highly ordered proteins. Other proteins,
however, are almost entirely without secondary structure and exist as
unfolded polypeptide chains in the cytosol.
(A)
50 nm
(B)
Figure 4–18 Stacking of β sheets allows
some misfolded proteins to aggregate
into amyloid fibers. (A) Electron
micrograph shows an amyloid fiber formed
from a segment of a yeast prion protein.
ECB4 n4.103/4.18
(B) Schematic representation
shows the
stacking of β sheets that stabilize an
individual amyloid fiber. (A, courtesy of
David Eisenberg.)
Figure 4–19 Many proteins are composed
of separate functional domains. Elements
of secondary structure such as α helices
and β sheets pack together into stable,
independently folding, globular elements
called protein domains. A typical protein
molecule is built from one or more domains,
linked by a region of polypeptide chain
that is often relatively unstructured. The
ribbon diagram on the right represents the
bacterial transcription regulator protein
CAP, with one large domain (outlined in
blue) and one small domain (outlined in
yellow).
Intrinsically disordered sequences remained undetected for many years.
Their lack of folded structure makes them prime targets for the proteolytic enzymes that are released when cells are fractionated to isolate
their molecular components (see Panel 4–3, pp. 164–165). Unstructured
sequences also fail to form protein crystals and for this reason escape
the attention of X-ray crystallographers (see How We Know, pp. 162–
163). Indeed, the ubiquity of disordered sequences became appreciated
only after bioinformatics methods were developed that could recognize them from their amino acid sequences. Present estimates suggest
that a third of all eukaryotic proteins have long unstructured regions in
their polypeptide chain (greater than 30 amino acids in length), while a
substantial number of eukaryotic proteins are mostly disordered under
normal conditions.
Unstructured sequences have a variety of important functions in cells.
Being able to flex and bend, they can wrap around one or more target
proteins like a scarf, binding with both high specificity and low affinity
(Figure 4–21). By forming flexible tethers between the compact domains
in a protein, they provide flexibility while increasing the frequency of
encounters between the domains (Figure 4–21). They can help scaffold
proteins bring together proteins in an intracellular signaling pathway,
facilitating interactions (Figure 4–21). They also give proteins like elastin
α helix
β sheet
secondary
structure
single protein
domain
protein molecule
made of two
different domains
The Shape and Structure of Proteins
135
Figure 4–20 Ribbon models show
three different protein domains.
(A) Cytochrome b562 is a single-domain
protein involved in electron transfer in
E. coli. It is composed almost entirely of
α helices. (B) The NAD-binding domain
of the enzyme lactic dehydrogenase is
composed of a mixture of α helices and
β sheets. (C) An immunoglobulin domain
of an antibody molecule is composed of
a sandwich of two antiparallel β sheets. In
these examples, the α helices are shown in
green, while strands organized as β sheets
are denoted by red arrows. The protruding
loop regions (yellow) are often unstructured
and can provide binding sites for other
molecules. (Redrawn from originals courtesy
of Jane Richardson.)
(C)
(B)
(A)
the ability to form rubberlike fibers, allowing our tendons and skin to
recoil after being stretched. In addition to providing structural flexibility, unstructured sequences are also ideal substrates for the addition of
chemical groups that control the way many proteins behave—a topic we
discuss at length later in the chapter.
ECB4 m3.11/4.20
Few of the Many Possible Polypeptide Chains
Will Be Useful
In theory, a vast number of different polypeptide chains could be made
from 20 different amino acids. Because each amino acid is chemically
distinct and could, in principle, occur at any position, a polypeptide chain
four amino acids long has 20 × 20 × 20 × 20 = 160,000 different possible sequences. In other words, for a polypeptide that is n amino acids
long, 20n different chains are possible. For a typical protein length of 300
amino acids, more than 20300 (that’s 10390) different polypeptide chains
could theoretically be made.
Of the unimaginably large collection of potential polypeptide sequences,
only a miniscule fraction is actually present in cells. That’s because many
biological functions depend on proteins with stable, well-defined threedimensional conformations. This requirement restricts the list of possible
polypeptide sequences. Another constraint is that functional proteins
scaffold
protein
unstructured
region
+
structured
domain
reacting
proteins
BINDING
TETHERING DOMAINS
WITHIN A PROTEIN
TETHERING
INTERACTING PROTEINS
Figure 4–21 Unstructured regions of a
polypeptide chain in proteins can peform
many functions. A few of these functions
are illustrated here.
136
Chapter 4
Protein Structure and Function
Question 4–3
Random mutations only very rarely
result in changes in a protein that
improve its usefulness for the cell,
yet useful mutations are selected in
evolution. Because these changes
are so rare, for each useful mutation
there are innumerable mutations
that lead to either no improvement
or inactive proteins. Why, then, do
cells not contain millions of proteins
that are of no use?
must be “well-behaved” and not engage in unwanted associations with
other proteins in the cell—forming insoluble protein aggregates, for
example. Many potential proteins would therefore have been eliminated
by natural selection through the long trial-and-error process that underlies evolution (discussed in Chapter 9).
Thanks to this rigorous process of selection, the amino acid sequences of
many present-day proteins have evolved to guarantee that the polypeptide will adopt a stable conformation—one that bestows upon the protein
the exact chemical properties that will enable it to perform a particular function. Such proteins are so precisely built that a change in even
a few atoms in one amino acid can sometimes disrupt the structure of
a protein and thereby eliminate its function. In fact, the structures of
many proteins—and their constituent domains—are so stable and effective that they have been conserved throughout evolution among many
diverse organisms. The three-dimensional structures of the DNA-binding
domains from the yeast α2 protein and the Drosophila Engrailed protein,
for example, are almost completely superimposable, even though these
organisms are separated by more than a billion years of evolution. Other
proteins, however, have changed their structure and function over evolutionary time, as we now discuss.
Proteins Can Be Classified into Families
Once a protein had evolved a stable conformation with useful properties, its structure could be modified over time to enable it to perform
new functions. We know that this occurred quite often during evolution,
because many present-day proteins can be grouped into protein families, in which each family member has an amino acid sequence and a
three-dimensional conformation that closely resemble those of the other
family members.
Consider, for example, the serine proteases, a family of protein-cleaving
(proteolytic) enzymes that includes the digestive enzymes chymotrypsin,
trypsin, and elastase, as well as several proteases involved in blood clotting. When any two of these enzymes are compared, portions of their
amino acid sequences are found to be nearly the same. The similarity
of their three-dimensional conformations is even more striking: most of
the detailed twists and turns in their polypeptide chains, which are several hundred amino acids long, are virtually identical (Figure 4–22). The
various serine proteases nevertheless have distinct enzymatic activities,
each cleaving different proteins or the peptide bonds between different
types of amino acids.
Figure 4–22 Serine proteases constitute a
family of proteolytic enzymes. Backbone
models of two serine proteases, elastase
and chymotrypsin, are illustrated. Although
only those amino acid sequences in the
polypeptide chain shaded in green are
the same in the two proteins, the two
conformations are very similar nearly
everywhere. Nonetheless, the two proteases
prefer different substrates. The active site
of each enzyme—where its substrates are
bound and cleaved—is circled in red.
Serine proteases derive their name
from the amino acid serine, which directly
participates in the cleavage reaction. The
two black dots on the right side of the
chymotrypsin molecule mark the two ends
created where the enzyme has cleaved its
own backbone.
HOOC
HOOC
NH 2
elastase
NH 2
chymotrypsin
The Shape and Structure of Proteins
Large Protein Molecules Often Contain More Than
One Polypeptide Chain
The same type of weak noncovalent bonds that enable a polypeptide
chain to fold into a specific conformation also allow proteins to bind
to each other to produce larger structures in the cell. Any region on a
protein’s surface that interacts with another molecule through sets of
noncovalent bonds is termed a binding site. A protein can contain binding
sites for a variety of molecules, large and small. If a binding site recognizes the surface of a second protein, the tight binding of two folded
polypeptide chains at this site will create a larger protein, whose quaternary structure has a precisely defined geometry. Each polypeptide chain
in such a protein is called a subunit, and each subunit may contain more
than one domain.
In the simplest case, two identical, folded polypeptide chains form a symmetrical complex of two protein subunits (called a dimer ) that is held
together by interactions between two identical binding sites. The CAP
protein in bacterial cells is a dimer (Figure 4–23A) formed from two identical copies of the protein subunit shown previously in Figure 4–19. Many
other symmetrical protein complexes, formed from multiple copies of
the same polypeptide chain, are commonly found in cells. The enzyme
neuraminidase, for example, consists of a ring of four identical protein
subunits (Figure 4–23B).
tetramer of neuraminidase protein
dimer of the CAP protein
(A)
dimer formed by
interaction between
a single, identical
binding site on each
monomer
(B)
tetramer formed by
interactions between
two nonidentical binding
sites on each monomer
Figure 4–23 Many protein molecules contain multiple copies of the same protein subunit. (A) A symmetrical dimer. The CAP
protein is a complex of two identical polypeptide chains (see also Figure 4–19). (B) A symmetrical homotetramer. The enzyme
neuraminidase exists as a ring of four identical polypeptide chains. For both (A) and (B), a small schematic below the structure
emphasizes how the repeated use of the same binding interaction forms the structure. In (A), the use of the same binding site on each
monomer (represented by brown and green ovals) causes the formation of a symmetrical dimer. In (B), a pair of nonidentical binding
sites (represented by orange circles and blue squares) causes the formation of a symmetrical tetramer.
137
138
Chapter 4
Protein Structure and Function
Figure 4–24 Some proteins are formed as
a symmetrical assembly of two different
subunits. Hemoglobin, an oxygen-carrying
protein abundant in red blood cells,
contains two copies of α-globin (green) and
two copies of β-globin (blue). Each of these
four polypeptide chains contains a heme
molecule (red ), where oxygen (O2) is bound.
Thus, each molecule of hemoglobin in the
blood carries four molecules of oxygen.
β
α
β
α
Other proteins contain two or more different polypeptide chains.
Hemoglobin, the protein that carries oxygen in red blood cells, is a particularly well-studied example. The protein contains two identical α-globin
ECB2
e4.20/4.20
subunits and two identical
β-globin
subunits, symmetrically arranged
(Figure 4–24). Many proteins contain multiple subunits, and they can be
very large (Movie 4.5).
Proteins Can Assemble into Filaments, Sheets, or Spheres
Proteins can form even larger assemblies than those discussed so far.
Most simply, a chain of identical protein molecules can be formed if
the binding site on one protein molecule is complementary to another
region on the surface of another protein molecule of the same type.
Because each protein molecule is bound to its neighbor in an identical
way (see Figure 4–14), the molecules will often be arranged in a helix
that can be extended indefinitely in either direction (Figure 4–25). This
type of arrangement can produce an extended protein filament. An actin
filament, for example, is a long, helical structure formed from many molecules of the protein actin (Figure 4–26). Actin is extremely abundant
in eukaryotic cells, where it forms one of the major filament systems of
the cytoskeleton (discussed in Chapter 17). Other sets of identical proteins associate to form tubes, as in the microtubules of the cytoskeleton
(Figure 4–27), or cagelike spherical shells, as in the protein coats of virus
particles (Figure 4–28).
(A)
free
subunits
assembled
structures
dimer
binding
site
(B)
helix
binding
sites
(C)
ring
binding
sites
Many large structures, such as viruses and ribosomes, are built from a
mixture of one or more types of protein plus RNA or DNA molecules.
These structures can be isolated in pure form and dissociated into their
constituent macromolecules. It is often possible to mix the isolated components back together and watch them reassemble spontaneously into
the original structure. This demonstrates that all the information needed
for assembly of the complicated structure is contained in the macromolecules themselves. Experiments of this type show that much of the
Figure 4–25 Identical protein subunits can assemble into complex
structures. (A) A protein with just one binding site can form a dimer
with another identical protein. (B) Identical proteins with two different
binding sites will often form a long, helical filament. (C) If the two
binding sites are disposed appropriately in relation to each other, the
protein subunits will form a closed ring instead of a helix (see also
Figure 4–23B).
The Shape and Structure of Proteins
Figure 4–26 An actin filament is
composed of identical protein subunits.
The helical array of actin molecules in
a filament often contains thousands of
molecules and extends for micrometers in
the cell.
50 nm
structure of a cell is self-organizing: if the required proteins are produced
in the right amounts, the appropriate structures will form automatically.
Some Types of Proteins Have Elongated Fibrous Shapes
Most of the proteins we have discussed so far are globular proteins, in
which the polypeptide chain folds up into a compact shape like a ball with
an irregular surface. Enzymes, for example, tend to be globular proteins:
even though many are large and complicated, with multiple subunits,
most have a quaternary structure
with an overall rounded shape (see
ECB4 m3.25/4.25
Figure 4–11). In contrast, other proteins have roles in the cell that require
them to span a large distance. These proteins generally have a relatively simple, elongated three-dimensional structure and are commonly
referred to as fibrous proteins.
One large class of intracellular fibrous proteins resembles α-keratin,
which we met earlier when we introduced the α-helix. Keratin filaments
are extremely stable: long-lived structures such as hair, horns, and nails
are composed mainly of this protein. An α-keratin molecule is a dimer
of two identical subunits, with the long α helices of each subunit forming a coiled-coil (see Figure 4–16). These coiled-coil regions are capped
at either end by globular domains containing binding sites that allow
them to assemble into ropelike intermediate filaments—a component
of the cytoskeleton that gives cells mechanical strength (discussed in
Chapter 17).
Fibrous proteins are especially abundant outside the cell, where they
form the gel-like extracellular matrix that helps bind cells together to form
tissues. These proteins are secreted by the cells into their surroundings,
where they often assemble into sheets or long fibrils. Collagen is the most
abundant of these fibrous extracellular proteins in animal tissues. A collagen molecule consists of three long polypeptide chains, each containing
the nonpolar amino acid glycine at every third position. This regular structure allows the chains to wind around one another to generate a long,
regular, triple helix with glycine at its core (Figure 4–29A). Many such
filament
subunit
spherical
shell
hollow
tube
Figure 4–27 A single type of protein subunit can pack together to form a
filament, a hollow tube, or a spherical shell. Actin subunits, for example, form
actin filaments (see Figure 4–26), whereas tubulin subunits form hollow microtubules,
and some virus proteins form a spherical
shell (capsid) that encloses the viral genome
ECB4 e4.23/4.26
(see Figure 4–28).
139
140
Chapter 4
Protein Structure and Function
collagen molecules bind to one another side-by-side and end-to-end to
create long overlapping arrays called collagen fibrils, which are extremely
strong and help hold tissues together, as described in Chapter 20.
In complete contrast to collagen is another fibrous protein in the extracellular matrix, elastin. Elastin molecules are formed from relatively loose
and unstructured polypeptide chains that are covalently cross-linked into
a rubberlike elastic meshwork. The resulting elastic fibers enable skin and
other tissues, such as arteries and lungs, to stretch and recoil without
tearing. As illustrated in Figure 4–29B, the elasticity is due to the ability
of the individual protein molecules to uncoil reversibly whenever they
are stretched.
20 nm
Figure 4–28 Many viral capsids are more
or less spherical protein assemblies.
They are formed from many copies of a
ECB4 m3.30/4.27
small set of protein
subunits. The nucleic
acid of the virus (DNA or RNA) is packaged
inside. The structure of the simian virus
SV40, shown here, was determined by X-ray
crystallography and is known in atomic
detail. (Courtesy of Robert Grant, Stephan
Crainic, and James M. Hogle.)
Extracellular Proteins Are Often Stabilized by Covalent
Cross-Linkages
Many protein molecules are either attached to the outside of a cell’s
plasma membrane or secreted as part of the extracellular matrix, which
exposes them to extracellular conditions. To help maintain their structures, the polypeptide chains in such proteins are often stabilized by
covalent cross-linkages. These linkages can either tie together two amino
acids in the same polypeptide chain or join together many polypeptide
chains in a large protein complex—as for the collagen fibrils and elastic
fibers just described.
The most common covalent cross-links in proteins are sulfur–sulfur
bonds. These disulfide bonds (also called S–S bonds) are formed before
a protein is secreted by an enzyme in endoplasmic reticulum that links
together two –SH groups from cysteine side chains that are adjacent in the
folded protein (Figure 4–30). Disulfide bonds do not change a protein’s
conformation, but instead act as a sort of “atomic staple” to reinforce
the protein’s most favored conformation. For example, lysozyme—an
elastic fiber
50 nm
short section of
collagen fibril
collagen
molecule
(300 nm × 1.5 nm)
STRETCH
1.5 nm
collagen
triple
helix
RELAX
single elastin molecule
cross-link
(A)
(B)
Figure 4–29 Collagen and elastin are abundant extracellular fibrous proteins. (A) A collagen molecule is a triple helix formed
by three extended protein chains that wrap around one another. Many rodlike collagen molecules are cross-linked together in the
extracellular space to form collagen fibrils (top), which have the tensile strength of steel. The striping on the collagen fibril is caused by
the regular repeating arrangement of the collagen molecules within the fibril. (B) Elastin molecules are cross-linked together by covalent
bonds (red ) to form rubberlike, elastic fibers. Each elastin polypeptide chain uncoils into a more extended conformation when the fiber
is stretched, and recoils spontaneously as soon as the stretching force is relaxed.
ECB4 m3.27/4.28
How Proteins Work
cysteine
polypeptide 1
C
C
CH2
CH2
SH
S
SH
C
CH2
SH
S
CH2
C
OXIDATION
REDUCTION
SH
CH2
C
CH2
C
C
interchain
disulfide
bond
CH2
S
S
intrachain
disulfide
bond
Figure 4–30 Disulfide bonds help stabilize
a favored protein conformation. This
diagram illustrates how covalent disulfide
bonds form between adjacent cysteine side
chains by the oxidation of their –SH groups.
As indicated, these cross-links can join
either two parts of the same polypeptide
chain or two different polypeptide chains.
Because the energy required to break one
covalent bond is much larger than the
energy required to break even a whole set
of noncovalent bonds (see Table 2–1, p. 48),
a disulfide bond can have a major stabilizing
effect on a protein’s folded structure
(Movie 4.6).
CH2
C
polypeptide 2
enzyme in tears, saliva, and other secretions that can disrupt bacterial
ECB4 e4.26/4.29
cell walls—retains its antibacterial activity for a long time because it is
stabilized by such disulfide cross-links.
Disulfide bonds generally do not form in the cell cytosol, where a high
concentration of reducing agents converts such bonds back to cysteine
–SH groups. Apparently, proteins do not require this type of structural
reinforcement in the relatively mild conditions in the cytosol.
How Proteins Work
As we have just seen, proteins are made from an enormous variety of
amino acid sequences and can fold into a unique shape. The surface
topography of a protein’s side chains endows each protein with a unique
function, based on its chemical properties. The union of structure, chemistry, and function gives proteins the extraordinary ability to orchestrate
the large number of dynamic processes that occur in cells.
Thus, for proteins, form and function are inextricably linked. But the
fundamental question remains: How do proteins actually work? In this
section, we will see that the activity of proteins depends on their ability
to bind specifically to other molecules, allowing them to act as catalysts,
structural supports, tiny motors, and so on. The examples we review here
by no means exhaust the vast functional repertoire of proteins. However,
the specialized functions of the proteins you will encounter elsewhere in
this book are based on the same principles.
All Proteins Bind to Other Molecules
The biological properties of a protein molecule depend on its physical
interaction with other molecules. Antibodies attach to viruses or bacteria
as part of the body’s defenses; the enzyme hexokinase binds glucose and
ATP to catalyze a reaction between them; actin molecules bind to one
another to assemble into long filaments; and so on. Indeed, all proteins
stick, or bind, to other molecules in a specific manner. In some cases, this
binding is very tight; in others, it is weak and short-lived. As we saw in
Chapter 3, the affinity of an enzyme for its substrate is reflected in its KM:
the lower the KM, the tighter the binding.
Regardless of its strength, the binding of a protein to other biological
molecules always shows great specificity: each protein molecule can bind
to just one or a few molecules out of the many thousands of different
141
Question 4–4
Hair is composed largely of fibers
of the protein keratin. Individual
keratin fibers are covalently crosslinked to one another by many
disulfide (S–S) bonds. If curly hair is
treated with mild reducing agents
that break a few of the cross-links,
pulled straight, and then oxidized
again, it remains straight. Draw a
diagram that illustrates the three
different stages of this chemical and
mechanical process at the level of
the keratin filaments, focusing on
the disulfide bonds. What do you
think would happen if hair were
treated with strong reducing agents
that break all the disulfide bonds?
142
Chapter 4
Protein Structure and Function
molecules it encounters. Any substance that is bound by a protein—
whether it is an ion, a small organic molecule, or a macromolecule—is
referred to as a ligand for that protein (from the Latin ligare, “to bind”).
noncovalent bonds
ligand
(A)
The ability of a protein to bind selectively and with high affinity to a ligand
is due to the formation of a set of weak, noncovalent interactions—hydrogen bonds, electrostatic attractions, and van der Waals attractions—plus
favorable hydrophobic forces (see Panel 2–7, pp. 78–79). Each individual noncovalent interaction is weak, so that effective binding requires
many such bonds to be formed simultaneously. This is possible only if
the surface contours of the ligand molecule fit very closely to the protein,
matching it like a hand in a glove (Figure 4–31).
protein
When molecules have poorly matching surfaces, few noncovalent interactions occur, and the two molecules dissociate as rapidly as they come
together. This is what prevents incorrect and unwanted associations
from forming between mismatched molecules. At the other extreme,
when many noncovalent interactions are formed, the association can
persist for a very long time. Strong binding between molecules occurs in
cells whenever a biological function requires that the molecules remain
tightly associated for a long time—for example, when a group of macromolecules come together to form a functional subcellular structure such
as a ribosome.
(B)
Figure 4–31 The binding of a protein to
another molecule is highly selective. Many
weak interactions are needed to enable a
protein to bind tightly to a second molecule
(a ligand). The
must therefore fit
ECB4ligand
e4.27/4.30
precisely into the protein’s binding site, like
a hand into a glove, so that a large number
of noncovalent interactions can be formed
between the protein and the ligand.
(A) Schematic drawing shows the binding of
a hypothetical protein and ligand; (B) spacefilling model.
The region of a protein that associates with a ligand, known as its binding site, usually consists of a cavity in the protein surface formed by a
particular arrangement of amino acid side chains. These side chains can
belong to amino acids that are widely separated on the linear polypeptide chain, but are brought together when the protein folds (Figure 4–32).
Other regions on the surface often provide binding sites for different ligands that regulate the protein’s activity, as we discuss later. Yet other
parts of the protein may be required to attract or attach the protein to a
particular location in the cell—for example, the hydrophobic α helix of a
amino acid
side chains
H
C
N
O
H
C
H
C
unfolded protein
FOLDING
CH2
hydrogen bond
O
H
(CH2)3
NH
C
arginine
binding site
serine
O
O
+
NH2
NH2
cyclic AMP bound to
folded protein
5′
P
O
O
O
N
H
serine
3′
N
O
H
N
_
O
electrostatic
attraction
N
C
O
N
N
(A)
(B)
CH2
C
H
O
CH2
C
H
H
H
O
threonine
CH
H 3C
C
CH2 glutamic
folded protein
H
acid
H
H
Figure 4–32 Binding sites allow proteins to interact with specific ligands. (A) The folding of the polypeptide chain typically creates a
crevice or cavity on the folded protein’s surface, where specific amino acid side chains are brought together in such a way that they can
form a set of noncovalent bonds only with certain ligands. (B) Close-up view of an actual binding site showing the hydrogen bonds and an
electrostatic interaction formed between a protein and its ligand (in this example, the bound ligand is cyclic AMP, shown in dark brown).
ECB4 e4.28/4.31
How Proteins Work
143
membrane-spanning protein allows it to be inserted into the lipid bilayer
of a cell membrane (discussed in Chapter 11).
Although the atoms buried in the interior of a protein have no direct
contact with the ligand, they provide an essential scaffold that gives the
surface its contours and chemical properties. Even tiny changes to the
amino acids in the interior of a protein can change the protein’s threedimensional shape and destroy its function.
There Are Billions of Different Antibodies, Each with a
Different Binding Site
Figure 4–33 An antibody is Y-shaped
and has two identical antigen-binding
sites, one on each arm of the Y.
(A) Schematic drawing of a typical antibody
molecule. The protein is composed of four
polypeptide chains (two identical heavy
chains and two identical and smaller light
chains), held together by disulfide bonds
(red). Each chain is made up of several
similar domains, here shaded either blue
or gray. The antigen-binding site is formed
where a heavy-chain variable domain (VH)
and a light-chain variable domain (VL) come
close together. These are the domains that
differ most in their amino acid sequence
in different antibodies—hence their name.
(B) Ribbon drawing of a single light chain
showing that the most variable parts of the
polypeptide chain (orange) extend as loops
at one end of the variable domain (VL) to
form half of one antigen-binding site of the
antibody molecule shown in (A). Note that
both the constant and variable domains are
composed of a sandwich of two antiparallel
β sheets (see also Figure 4–20C), connected
by a disulfide bond (red ).
All proteins must bind to particular ligands to carry out their various functions. For antibodies, the universe of possible ligands is limitless. Each of
us has the capacity to produce a huge variety of antibodies, among which
there will be one that is capable of recognizing and binding tightly to
almost any molecule imaginable.
Antibodies are immunoglobulin proteins produced by the immune system in response to foreign molecules, especially those on the surface
of an invading microorganism. Each antibody binds to a particular target molecule extremely tightly, either inactivating the target directly or
marking it for destruction. An antibody recognizes its target molecule—
called an antigen—with remarkable specificity, and, because there are
potentially billions of different antigens that a person might encounter,
we have to be able to produce billions of different antibodies.
Antibodies are Y-shaped molecules with two identical antigen-binding
sites, each of which is complementary to a small portion of the surface
of the antigen molecule. A detailed examination of the antigen-binding
sites of antibodies reveals that they are formed from several loops of
polypeptide chain that protrude from the ends of a pair of closely juxtaposed protein domains (Figure 4–33). The amino acid sequence in these
antigenbinding
site
heavy chain
antigen
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S
S S
S S
S
VL domain
NH2
S
light chain
hypervariable
loops that
bind antigen
VH domain
S
S
variable domain
of light chain (VL)
5 nm
S
S
S
S
(A)
HOOC
disulfide
bond
constant domain
of light chain
(B)
144
Chapter 4
Protein Structure and Function
loops can vary greatly without altering the basic structure of the antibody. An enormous diversity of antigen-binding sites can be generated by
changing only the length and amino acid sequence of the loops, which is
how the wide variety of different antibodies is formed (Movie 4.7).
With their unique combination of specificity and diversity, antibodies are
not only indispensable for fighting off infections, they are also invaluable
in the laboratory, where they can be used to identify, purify, and study
other molecules (Panel 4–2, pp. 146–147).
Enzymes Are Powerful and Highly Specific Catalysts
Question 4–5
Use drawings to explain how
an enzyme (such as hexokinase,
mentioned in the text) can
distinguish its normal substrate (here
d-glucose) from the optical isomer
l-glucose, which is not a substrate.
(Hint: remembering that a carbon
atom forms four single bonds
that are tetrahedrally arranged
and that the optical isomers are
mirror images of each other around
such a bond, draw the substrate
as a simple tetrahedron with four
different corners and then draw its
mirror image. Using this drawing,
indicate why only one optical isomer
might bind to a schematic active site
of an enzyme.)
For many proteins, binding to another molecule is their main function.
An actin molecule, for example, need only associate with other actin
molecules to form a filament. There are proteins, however, for which ligand binding is simply a necessary first step in their function. This is the
case for the large and very important class of proteins called enzymes.
These remarkable molecules are responsible for nearly all of the chemical transformations that occur in cells. Enzymes bind to one or more
ligands, called substrates, and convert them into chemically modified
products, doing this over and over again with amazing rapidity. As we
saw in Chapter 3, they speed up reactions, often by a factor of a million or more, without themselves being changed—that is, enzymes act as
catalysts that permit cells to make or break covalent bonds at will. This
catalysis of organized sets of chemical reactions by enzymes creates and
maintains the cell, making life possible.
Enzymes can be grouped into functional classes based on the chemical reactions they catalyze (Table 4–1). Each type of enzyme is highly
specific, catalyzing only a single type of reaction. Thus, hexokinase adds
a phosphate group to d-glucose but not to its optical isomer l-glucose;
the blood-clotting enzyme thrombin cuts one type of blood-clotting protein between a particular arginine and its adjacent glycine and nowhere
Table 4–1 Some Common Functional Classes of Enzymes
Enzyme Class
Biochemical Function
Hydrolase
General term for enzymes that catalyze a hydrolytic cleavage reaction
Nuclease
Breaks down nucleic acids by hydrolyzing bonds between nucleotides
Protease
Breaks down proteins by hydrolyzing peptide bonds between amino acids
Ligase
Joins two molecules together; DNA ligase joins two DNA strands together end-to-end
Isomerase
Catalyzes the rearrangement of bonds within a single molecule
Polymerase
Catalyzes polymerization reactions such as the synthesis of DNA and RNA
Kinase
Catalyzes the addition of phosphate groups to molecules. Protein kinases are an important group of kinases
that attach phosphate groups to proteins
Phosphatase
Catalyzes the hydrolytic removal of a phosphate group from a molecule
Oxido-reductase
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is
reduced. Enzymes of this type are often called oxidases, reductases, or dehydrogenases
ATPase
Hydrolyzes ATP. Many proteins have an energy-harnessing ATPase activity as part of their function, including
motor proteins such as myosin (discussed in Chapter 17) and membrane transport proteins such as the
sodium pump (discussed in Chapter 12)
Enzyme names typically end in “-ase,” with the exception of some enzymes, such as pepsin, trypsin, thrombin, lysozyme, and so on,
which were discovered and named before the convention became generally accepted at the end of the nineteenth century. The name
of an enzyme usually indicates the nature of the reaction catalyzed. For example, citrate synthase catalyzes the synthesis of citrate by a
reaction between acetyl CoA and oxaloacetate.
How Proteins Work
145
else. As discussed in detail in Chapter 3, enzymes often work in tandem,
with the product of one enzyme becoming the substrate for the next. The
result is an elaborate network of metabolic pathways that provides the cell
with energy and generates the many large and small molecules that the
cell needs.
Lysozyme Illustrates How an Enzyme Works
To explain how enzymes catalyze chemical reactions, we will use the
example of lysozyme—an enzyme that acts as a natural antibiotic in egg
white, saliva, tears, and other secretions. Lysozyme severs the polysaccharide chains that form the cell walls of bacteria. Because the bacterial
cell is under pressure due to intracellular osmotic forces, cutting even a
small number of polysaccharide chains causes the cell wall to rupture
and the bacterium to burst, or lyse. Lysozyme is a relatively small and
stable protein, which can be isolated easily in large quantities. For these
reasons it has been intensively studied, and it was the first enzyme whose
structure was worked out in atomic detail by X-ray crystallography.
The reaction catalyzed by lysozyme is a hydrolysis: the enzyme adds a
molecule of water to a single bond between two adjacent sugar groups in
the polysaccharide chain, thereby causing the bond to break. The reaction
is energetically favorable because the free energy of the severed polysaccharide chain is lower than the free energy of the intact chain. However,
the pure polysaccharide can sit for years in water without being hydrolyzed to any detectable degree. This is because there is an energy barrier
to such reactions, called the activation energy (discussed in Chapter 3,
pp. 91–93). For a colliding water molecule to break a bond linking two
sugars, the polysaccharide molecule has to be distorted into a particular
shape—the transition state—in which the atoms around the bond have
an altered geometry and electron distribution. To distort the polysaccharide in this way requires a large input of energy from random molecular
collisions. In aqueous solution at room temperature, the energy of such
collisions almost never exceeds the activation energy; therefore, hydrolysis occurs extremely slowly, if at all.
This is where the enzyme comes in. Like all enzymes, lysozyme has a
binding site on its surface, termed an active site, that cradles the contours of its substrate molecule. Here, the catalysis of the chemical reaction
occurs. Because its substrate is a polymer, lysozyme’s active site is a long
groove that holds six linked sugars in the polysaccharide chain at the
same time. As soon as the enzyme–substrate complex forms, the enzyme
cuts the polysaccharide by catalyzing the addition of a water molecule to
one of its sugar–sugar bonds. The severed chain is then quickly released,
freeing the enzyme for further cycles of cleavage (Figure 4–34).
The chemistry that underlies the binding of lysozyme to its substrate is
the same as that for antibody binding to its antigen: the formation of
+
+
(A)
S
Figure 4–34 Lysozyme cleaves a
polysaccharide chain. (A) Schematic view
of the enzyme lysozyme (E), which catalyzes
the cutting of a polysaccharide substrate
molecule (S). The enzyme first binds to
the polysaccharide to form an enzyme–
substrate complex (ES), then it catalyzes the
cleavage of a specific covalent bond
in the backbone of the polysaccharide.
The resulting enzyme–product complex
(EP) rapidly dissociates, releasing the
products (P) and leaving the enzyme free
to act on another substrate molecule.
(B) A space-filling model of lysozyme bound
to a short length of polysaccharide chain
prior to cleavage. (B, courtesy of
Richard J. Feldmann.)
+
E
ES
EP
E+P
(B)
146
Panel 4–2
MAKING AND USING ANTIBODIES
THE ANTIBODY MOLECULE
antigen-binding sites
light chain
Antibodies are proteins
that bind very tightly to
their targets (antigens).
They are produced in
vertebrates as a defense
against infection. Each
antibody molecule is
made of two identical
light chains and two
identical heavy chains,
so the two antigenbinding sites are
identical.
hinge
heavy chain
5 nm
ANTIBODY SPECIFICITY
heavy chain
antigen
B CELLS PRODUCE ANTIBODIES
light chain
Antibodies are made by a class of white blood cells called B
lymphocytes, or B cells. Each resting B cell carries a different
membrane-bound antibody molecule on its surface that serves
as a receptor for recognizing a specific antigen. When antigen
binds to this receptor, the B cell is stimulated to divide and to
secrete large amounts of the same antibody in a soluble form.
different B cells
Antigen binds to
B cell displaying an
antibody that fits
the antigen.
An individual human
can make billions of
different antibody
molecules, each with a
distinct antigen-binding
site. Each antibody
recognizes its antigen
with great specificity.
The B cell is stimulated both to proliferate and to make
and secrete more of same antibody.
RAISING ANTIBODIES IN ANIMALS
Antibodies can be made in the laboratory by injecting an animal
(usually a mouse, rabbit, sheep, or goat) with antigen A.
ANTIBODIES DEFEND US AGAINST INFECTION
foreign
molecules
viruses
A
bacteria
inject antigen A
amount of anti-A
antibodies in blood
ANTIBODIES ( ) CROSS-LINK ANTIGENS INTO AGGREGATES
take blood later
Repeated injections of the same antigen at intervals of several
weeks stimulate specific B cells to secrete large amounts of
anti-A antibodies into the bloodstream.
A
Antibody–antigen
aggregates are ingested
by phagocytic cells.
Special proteins in
blood kill antibodycoated bacteria
or viruses.
A
A
time
Because many different B cells are stimulated by antigen A, the
blood will contain a variety of anti-A antibodies, each of which
binds A in a slightly different way.
How Proteins Work
USING ANTIBODIES TO PURIFY MOLECULES
mixture of molecules
IMMUNOAFFINITY
COLUMN
CHROMATOGRAPHY
E
FN
P A O
A
M K C
H DR
B
J S
L
Q AG
R
P M
D N
Q O K
B
H
J
S A
G A
C
F L
A
E
IMMUNOPRECIPITATION
bead coated with
anti-A antibodies
mixture of molecules
147
elute antigen A
from beads
A
A
add specific
anti-A antibodies
A
A
A
A A
column packed
with these beads
C K
RN
etc
A
A
discard flow-through
collect pure antigen A
collect aggregate of A molecules and
anti-A antibodies by centrifugation
MONOCLONAL ANTIBODIES
USING ANTIBODIES AS MOLECULAR TAGS
Large quantities of a single type of antibody
molecule can be obtained by fusing a B cell
(taken from an animal injected with antigen A)
with a tumor cell. The resulting hybrid cell
divides indefinitely and secretes anti-A
antibodies of a single (monoclonal) type.
FUSE ANTIBODY-SECRETING
B CELL WITH TUMOR CELL
Hybrid cell
makes and
secretes anti-A
antibody and
divides
indefinitely.
MICROSCOPIC DETECTION
Tumor cells in
culture divide
indefinitely but
do not make
antibody.
specific antibodies
against antigen A
labeled antibodies
cell
wall
50 µm
Fluorescent antibody binds to
antigen A in tissue and is detected
in a fluorescence microscope. The
antigen here is pectin in the cell
walls of a slice of plant tissue.
BIOCHEMICAL DETECTION
B cell from animal
injected with antigen
A makes anti-A
antibody but does
not divide forever.
couple to fluorescent dye,
gold particle, or other
special tag
Antigen A is
separated from
other molecules
by electrophoresis.
Note: In all cases, the sensitivity can
be greatly increased by using multiple
layers of antibodies. This “sandwich”
method enables smaller numbers of
antigen molecules to be detected.
ECB4 Panel 4.03b
200 nm
Gold-labeled antibody binds to
antigen A in tissue and is detected
in an electron microscope. The
antigen is pectin in the cell wall
of a single plant cell.
Incubation with the
labeled antibodies
that bind to antigen A
allows the position of the
antigen to be determined.
Labeled second antibody
(blue) binds to first
antibody (black).
antigen
148
Chapter 4
Protein Structure and Function
SUBSTRATE
PRODUCTS
This substrate is an oligosaccharide of six sugars,
labeled A through F. Only sugars D and E are shown in detail.
R
AB C
O
D
R
CH2OH
E
O
O
CH2OH
O
O
R
C
H
O
C
R
H
O
C
C
O
C1 carbon
H
D
O
O
CH2OH
E
O
F
C
C
O
O
H
O
O
R
O
H
CH2OH
O
E
HOCH2
O
O
O
D
C
H H
O
O O
C
R
R
O
O
Asp 52
O
O
R
R
O
O
O
HOCH2
O
H
Glu 35
C
E
O
C
O
CH2OH
D
H
CH2OH
Glu 35
H
HOCH2
O
side chain
on sugar E
O
D
AB C
F
C
Glu 35
O
The final products are an oligosaccharide of four sugars
(left) and a disaccharide (right), produced by hydrolysis.
CH2OH
E
O
O
R
H
O
C
C
O
Asp 52
C
C
Asp 52
ES
TRANSITION STATE
EP
In the enzyme–substrate complex (ES), the
enzyme forces sugar D into a strained
conformation. The Glu 35 in the enzyme is
positioned to serve as an acid that attacks the
adjacent sugar–sugar bond by donating a proton
(H+ ) to sugar E; Asp 52 is poised to attack the
C1 carbon atom of sugar D.
The Asp 52 has formed a covalent bond between
the enzyme and the C1 carbon atom of sugar D.
The Glu 35 then polarizes a water molecule (red),
so that its oxygen can readily attack the C1
carbon atom of sugar D and displace Asp 52.
The reaction of the water molecule (red)
completes the hydrolysis and returns the enzyme
to its initial state, forming the final enzyme–
product complex (EP).
Figure 4–35 Enzymes bind to, and
chemically alter, substrate molecules.
In the active site of lysozyme, a covalent
bond in a polysaccharide molecule is bent
and then broken. The top row shows the
free substrate and the free products. The
three lower panels depict sequential events
at the enzyme active site, during which a
sugar–sugar covalent bond is broken. Note
the change in the conformation of sugar D
in the enzyme–substrate complex compared
with the free substrate. This conformation
favors the formation of the transition state
shown in the middle panel, greatly lowering
the activation energy required for the
reaction. The reaction, and the structure of
lysozyme bound to its product, are shown in
Movie 4.8 and Movie 4.9. (Based on
D.J. Vocadlo et al., Nature 412:835–838,
2001.)
multiple noncovalent bonds. However, lysozyme holds its polysaccharide
substrate
in such a way that one of the two sugars involved in the bond
ECB4 m3.51/4.34
to be broken is distorted from its normal, most stable conformation. The
bond to be broken is held close to two specific amino acids with acidic
side chains—a glutamic acid and an aspartic acid—located within the
active site of the enzyme. Conditions are thereby created in the microenvironment of the lysozyme active site that greatly reduce the activation
energy necessary for the hydrolysis to take place (Figure 4–35). The overall chemical reaction, from the initial binding of the polysaccharide on the
surface of the enzyme to the final release of the severed chains, occurs
many millions of times faster than it would in the absence of enzyme.
Other enzymes use similar mechanisms to lower the activation energies
and speed up the reactions they catalyze. In reactions involving two or
more substrates, the active site also acts like a template or mold that
brings the reactants together in the proper orientation for the reaction
to occur (Figure 4–36A). As we saw for lysozyme, the active site of an
enzyme contains precisely positioned chemical groups that speed up the
reaction by altering the distribution of electrons in the substrates (Figure
4–36B). Binding to the enzyme also changes the shape of the substrate,
bending bonds so as to drive the bound molecule toward a particular
transition state (Figure 4–36C). Finally, like lysozyme, many enzymes
participate intimately in the reaction by briefly forming a covalent bond
between the substrate and an amino acid side chain in the active site.
Subsequent steps in the reaction restore the side chain to its original
state, so the enzyme remains unchanged after the reaction and can go on
to catalyze many more reactions.
How Proteins Work
+
–
+
(A) enzyme binds to two
substrate molecules and
orients them precisely to
encourage a reaction to
occur between them
Figure 4–36 Enzymes can encourage
a reaction in several ways. (A) Holding
reacting substrates together in a precise
alignment. (B) Rearranging the distribution
of charge in a reaction intermediate.
(C) Altering bond angles in the substrate to
increase the rate of a particular reaction.
–
(B) binding of substrate
to enzyme rearranges
electrons in the substrate,
creating partial negative
and positive charges
that favor a reaction
149
(C) enzyme strains the
bound substrate
molecule, forcing it
toward a transition
state to favor a reaction
Many Drugs Inhibit Enzymes
Many of the drugs we take to treat or prevent illness work by blocking the
activity of a particular enzyme. Cholesterol-lowering statins inhibit HMGCoA reductase, an enzyme involved in the synthesis of cholesterol by
the liver. Methotrexate kills some types of cancer cells by shutting down
dihydrofolate reductase, an enzyme that produces a compound required
for DNA synthesis during cell division. Because cancer cells have lost
important intracellular control systems, some of them are unusually sensitive to treatments that interrupt chromosome replication, making them
ECB4 m3.52/4.35
susceptible to methotrexate.
Pharmaceutical companies often develop drugs by first using automated
methods to screen massive libraries of compounds to find chemicals that
are able to inhibit the activity of an enzyme of interest. They can then
chemically modify the most promising compounds to make them even
more effective, enhancing their binding affinity and specificity for the target enzyme. As we discuss in Chapter 20, the anticancer drug Gleevec®
was designed to specifically inhibit an enzyme whose aberrant behavior is required for the growth of a type of cancer called chronic myeloid
leukemia. The drug binds tightly in the substrate-binding pocket of the
enzyme, blocking its activity (see Figure 20–56).
Tightly Bound Small Molecules Add Extra Functions to
Proteins
Although the order of amino acids in proteins gives these macromolecules their shape and functional versatility, sometimes the amino acids
by themselves are not enough for a protein to do its job. Just as we use
tools to enhance and extend the capabilities of our hands, so proteins
often employ small, nonprotein molecules to perform functions that
would be difficult or impossible using amino acids alone. Thus, the photoreceptor protein rhodopsin, which is the light-sensitive protein made
by the rod cells in the retina, detects light by means of a small molecule,
retinal, which is attached to the protein by a covalent bond to a lysine side
chain (Figure 4–37A). Retinal changes its shape when it absorbs a photon
of light, and this change is amplified by rhodopsin to trigger a cascade of
reactions that eventually leads to an electrical signal being carried to the
brain.
Another example of a protein that contains a nonprotein portion essential
for its function is hemoglobin (see Figure 4–24). A molecule of hemoglobin
carries four noncovalently bound heme groups, ring-shaped molecules
each with a single central iron atom (Figure 4–37B). Heme gives hemoglobin (and blood) its red color. By binding reversibly to dissolved oxygen
gas through its iron atom, heme enables hemoglobin to pick up oxygen
in the lungs and release it in tissues that need it.
150
Chapter 4
Protein Structure and Function
Figure 4–37 Retinal and heme are
required for the function of certain
proteins. (A) The structure of retinal, the
light-sensitive molecule covalently attached
to the rhodopsin protein in our eyes. (B) The
structure of a heme group, shown with the
carbon-containing heme ring colored red
and the iron atom at its center in orange.
A heme group is tightly, but noncovalently,
bound to each of the four polypeptide
chains in hemoglobin, the oxygen-carrying
protein whose structure was shown in
Figure 4–24.
H3C CH3
CH3
H3C
COOH
COOH
CH2
CH2
CH2
CH2
CH3
+N
N
Fe
CH3
H2C
H3C
CHO
(A)
H
C
N+
CH3
(B)
N
CH3
HC
CH2
When these small molecules are attached to their protein, they become
an integral part of the protein molecule itself. We discuss in Chapter 11
how proteins can be anchored to cell membranes through covalently
attached lipid molecules, and how proteins that are either secreted from
the cell or bound to its surface can be modified by the covalent addition
of sugars and oligosaccharides.
Enzymes, too, make useECB4
of nonprotein
molecules: they frequently have
m3.53/4.36
a small molecule or metal atom associated with their active site that
assists with their catalytic function. Carboxypeptidase, an enzyme that
cuts polypeptide chains, carries a tightly bound zinc ion in its active site.
During the cleavage of a peptide bond by carboxypeptidase, the zinc ion
forms a transient bond with one of the substrate atoms, thereby assisting the hydrolysis reaction. In other enzymes, a small organic molecule
serves a similar purpose. Biotin, for example, is found in enzymes that
transfer a carboxyl group (–COO–) from one molecule to another (see
Figure 3–37). Biotin participates in these reactions by forming a transient
covalent bond to the –COO– group to be transferred, thereby forming an
activated carrier (see Table 3–2, p. 112). This small molecule is better
suited for this function than any of the amino acids used to make proteins.
Because biotin cannot be synthesized by humans, it must be provided in
the diet; thus biotin is classified as a vitamin. Other vitamins are similarly
needed to make small molecules that are essential components of our
proteins; vitamin A, for example, is needed in the diet to make retinal, the
light-sensitive part of rhodopsin just discussed.
How Proteins Are Controlled
So far, we have examined how proteins do their jobs: how binding to
other proteins or small molecules allows them to perform their specific
functions. But inside the cell, most proteins and enzymes do not work
continuously, or at full speed. Instead, their activities are regulated in a
coordinated fashion so the cell can maintain itself in an optimal state,
producing only those molecules it requires to thrive under the current
conditions. By coordinating when—and how vigorously—proteins function, the cell ensures that it does not deplete its energy reserves by
accumulating molecules it does not need or waste its stockpiles of critical substrates. We now consider how cells control the activity of their
enzymes and other proteins.
The regulation of protein activity occurs at many levels. At one level, the
cell controls the amount of the protein it contains. It can do so by regulating the expression of the gene that encodes that protein (discussed in
Chapter 8), and by regulating the rate at which the protein is degraded
How Proteins Are Controlled
(discussed in Chapter 7). At another level, the cell controls enzymatic
activities by confining sets of enzymes to particular subcellular compartments, often—but not always—enclosed by distinct membranes
(discussed in Chapters 14 and 15). But the most rapid and general mechanism used to adjust the activity of a protein occurs at the level of the
protein itself. Although proteins can be switched on or off in various
ways, as we see next, all of these mechanisms cause the protein to alter
its shape, and therefore its function.
The Catalytic Activities of Enzymes Are Often Regulated
by Other Molecules
A living cell contains thousands of different enzymes, many of which
are operating at the same time in the same small volume of the cytosol.
By their catalytic action, enzymes generate a complex web of metabolic
pathways, each composed of chains of chemical reactions in which the
product of one enzyme becomes the substrate of the next. In this maze of
pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate
controls are required to regulate when and how rapidly each reaction
occurs.
A
B
C
X
feedback
inhibitor
Y
Z
Figure 4–38 Feedback inhibition regulates
the flow through biosynthetic pathways.
B is the first metabolite in a pathway that
gives the end product Z. Z inhibits the first
enzyme that is specific to its own synthesis
and thereby limits
own concentration in
ECB4 its
m3.56/4.37
the cell. This form of negative regulation is
called feedback inhibition.
A common type of control occurs when a molecule other than a substrate
specifically binds to an enzyme at a special regulatory site, altering the
rate at which the enzyme converts its substrate to product. In feedback
inhibition, for example, an enzyme acting early in a reaction pathway is
inhibited by a late product of that pathway. Thus, whenever large quantities of the final product begin to accumulate, the product binds to an
earlier enzyme and slows down its catalytic action, limiting further entry
of substrates into that reaction pathway (Figure 4–38). Where pathways
branch or intersect, there are usually multiple points of control by different final products, each of which works to regulate its own synthesis
(Figure 4–39). Feedback inhibition can work almost instantaneously and
is rapidly reversed when product levels fall.
Feedback inhibition is a negative regulation: it prevents an enzyme from
acting. Enzymes can also be subject to positive regulation, in which the
enzyme’s activity is stimulated by a regulatory molecule rather than being
suppressed. Positive regulation occurs when a product in one branch
of the metabolic maze stimulates the activity of an enzyme in another
pathway.
Allosteric Enzymes Have Two or More Binding Sites That
Influence One Another
One feature of feedback inhibition was initially puzzling to those who
discovered it. Unlike what one expects to see for a competitive inhibitor
(see Figure 3–29), the regulatory molecule often has a shape that is totally
different from the shape of the enzyme’s preferred substrate. Indeed,
when this form of regulation was discovered in the 1960s, it was termed
allostery (from the Greek allo, “other,” and stere, “solid” or “shape”). As
more was learned about feedback inhibition, researchers realized that
many enzymes must have at least two different binding sites on their surface: the active site that recognizes the substrates and one or more sites
that recognize regulatory molecules. And that these sites must somehow
“communicate” to allow the catalytic events at the active site to be influenced by the binding of the regulatory molecule at its separate site.
The interaction between sites that are located in different regions on a
protein molecule is now known to depend on conformational changes in
the protein: binding of a ligand to one of the sites causes a shift in the protein’s structure from one folded shape to a slightly different folded shape,
151
Question 4–6
Consider the drawing in Figure
4–38. What will happen if, instead of
the indicated feedback,
A. Feedback inhibition from Z
affects the step B → C only?
B. Feedback inhibition from Z
affects the step Y → Z only?
C. Z is a positive regulator of the
step B → X?
D. Z is a positive regulator of the
step B → C?
For each case, discuss how useful
these regulatory schemes would be
for a cell.
152
Chapter 4
Protein Structure and Function
Figure 4–39 Feedback inhibition at
multiple points regulates connected
metabolic pathways. The biosynthetic
pathways for four different amino acids in
bacteria are shown, starting from the amino
acid aspartate. The red lines indicate points
at which products feed back to inhibit
enzymes and the blank boxes represent
intermediates in each pathway. In this
example, each amino acid controls the first
enzyme specific to its own synthesis, thereby
limiting its own concentrations and avoiding
a wasteful buildup of intermediates. Some
of the products also separately inhibit the
initial set of reactions common to all the
syntheses. Three different enzymes catalyze
the initial reaction from aspartate to aspartyl
phosphate, and each of these enzymes is
inhibited by a different product.
aspartate
aspartyl
phosphate
aspartate
semialdehyde
homoserine
lysine
threonine
methionine
isoleucine
which alters the binding of a ligand to a second site. Many enzymes have
two conformations that differ in activity, each stabilized by the binding
of different ligands. During feedback inhibition, for example, the binding
of an inhibitor at a regulatory site
the protein causes the protein to
MBoC6on
m3.57/4.38
shift to a conformation in which its active site—located elsewhere in the
protein—becomes less accommodating to the substrate molecule (Figure
4–40).
Many—if not most—protein molecules are allosteric: they can adopt two
or more slightly different conformations, and their activity can be regulated by a shift from one to another. This is true not only for enzymes
but also for many other proteins as well. The chemistry involved here
is extremely simple in concept: because each protein conformation will
have somewhat different contours on its surface, the protein’s binding
sites for ligands will be altered when the protein changes shape. Each ligand will stabilize the conformation that it binds to most strongly, and at
high enough concentrations a ligand will tend to “switch” the population
of proteins to the conformation that it favors (Figure 4–41).
Phosphorylation Can Control Protein Activity by
Causing a Conformational Change
Enzymes are regulated solely by the binding of small molecules. Another
method that eukaryotic cells use with great frequency to regulate protein
How Proteins Are Controlled
ON
OFF
bound CTP
molecule
CTP
regulatory
sites
5 nm
active site
INACTIVE ENZYME
ACTIVE ENZYME
activity involves attaching a phosphate group covalently to one or more
of the protein’s amino acid side chains. Because each phosphate group
carries two negative charges, the enzyme-catalyzed addition of a phosphate group can cause a major conformational change in a protein by, for
example, attracting a cluster of positively charged amino acid side chains
from somewhere else in the same protein. This conformational change
can, in turn, affect the binding of ligands elsewhere on the protein surface, thereby altering the protein’s activity. Removal of the phosphate
group by a second enzyme will
return
the protein to its original conforECB4
e4.36/4.39
mation and restore its initial activity.
This reversible protein phosphorylation controls the activity of many
types of proteins in eukaryotic cells; indeed, it is used so extensively that
more than one-third of the 10,000 or so proteins in a typical mammalian cell are phosphorylated at any one time. The addition and removal
of phosphate groups from specific proteins often occur in response to
signals that specify some change in a cell’s state. For example, the complicated series of events that takes place as a eukaryotic cell divides is
timed largely in this way (discussed in Chapter 18). And many of the
intracellular signaling pathways activated by extracellular signals such
as hormones depend on a network of protein phosphorylation events
(discussed in Chapter 16).
Protein phosphorylation involves the enzyme-catalyzed transfer of the
terminal phosphate group of ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain of the protein. This reaction is catalyzed
INACTIVE
ADP
ADP
sugar
(such as
glucose)
positive
regulation
ACTIVE
(A)
(B) without ADP, 10% active
(C) with ADP, 100% active
153
Figure 4–40 Feedback inhibition
triggers a conformational change in an
enzyme. The enzyme shown, aspartate
transcarbamoylase from E. coli, was used
in early studies of allosteric regulation.
This large multisubunit enzyme (see Figure
4–11) catalyzes an important reaction that
begins the synthesis of the pyrimidine
ring of C, U, and T nucleotides (see Panel
2–6, p. 76–77). One of the final products of
this pathway, cytosine triphosphate (CTP),
binds to the enzyme to turn it off whenever
CTP is plentiful. This diagram shows the
conformational change that occurs when the
enzyme is turned off by CTP binding to its
four regulatory sites, which are distinct from
the active site where the substrate binds.
Note that the aspartate transcarbamoylase
shown in Figure 4–11 is seen from the top.
This figure depicts the enzyme as seen from
the side.
Figure 4–41 The equilibrium between two
conformations of a protein is affected
by the binding of a regulatory ligand.
(A) Schematic diagram of a hypothetical,
allosterically regulated enzyme for which a
rise in the concentration of ADP molecules
(red wedges) increases the rate at which
the enzyme catalyzes the oxidation of sugar
molecules (blue hexagons). (B) With no
ADP present, only a small fraction of the
enzyme molecules spontaneously adopt
the active (closed) conformation; most
are in the inactive (open) conformation.
(C) Because ADP can bind to the protein
only in its closed, active conformation, an
increase in ADP concentration locks nearly
all of the enzyme molecules in the active
form. Such an enzyme could be used, for
example, to sense when ADP is building up
in the cell—which is usually a sign that ATP
is decreasing. In this way, the increase in
ADP would increase the oxidation of sugars
to provide more energy for the synthesis
of ATP from ADP—an example of positive
regulation.
154
Chapter 4
Protein Structure and Function
_
O
ATP
O
ADP
OH
serine
CH2
side chain
C
P
O
_
O
CH2
PROTEIN
KINASE
C
PROTEIN
PHOSPHATASE
Pi
(A)
kinase
phosphorylated
protein
P
OFF
ON
Pi
phosphatase
kinase
ON
(B)
P
by a protein kinase. The reverse reaction—removal of the phosphate
group, or dephosphorylation—is catalyzed by a protein phosphatase
(Figure 4–42A). Phosphorylation can either stimulate protein activity or
inhibit it, depending on the protein involved and the site of phosphorylation (Figure 4–42B). Cells contain hundreds of different protein kinases,
each responsible for phosphorylating a different protein or set of proteins. Cells also contain a smaller set of different protein phosphatases;
some of these are highly specific and remove phosphate groups from only
one or a few proteins, whereas others act on a broad range of proteins.
The state of phosphorylation of a protein at any moment in time, and thus
its activity, will depend on the relative activities of the protein kinases
and phosphatases that act on it.
For many proteins, a phosphate group is added to a particular side
chain and then removed in a continuous cycle. Phosphorylation cycles
of this kind allow proteins to switch rapidly from one state to another.
The more rapidly the cycle is “turning,” the faster the concentration of a
phosphorylated protein can change in response to a sudden stimulus that
increases its rate of phosphorylation. However, keeping the cycle turning
costs energy, because one molecule of ATP is hydrolyzed with each turn
of the cycle.
OFF
Pi
phosphatase
Figure 4–42 Protein phosphorylation is a
very common mechanism for regulating
protein activity. Many thousands of
proteins in a ECB4
typicale4.38/4.41
eukaryotic cell are
modified by the covalent addition of one
or more phosphate groups. (A) The general
reaction, shown here, entails transfer of a
phosphate group from ATP to an amino
acid side chain of the target protein by a
protein kinase. Removal of the phosphate
group is catalyzed by a second enzyme, a
protein phosphatase. In this example, the
phosphate is added to a serine side chain;
in other cases, the phosphate is instead
linked to the –OH group of a threonine or
tyrosine side chain. (B) Phosphorylation
can either increase or decrease the
protein’s activity, depending on the site of
phosphorylation and the structure of the
protein.
Covalent Modifications Also Control the Location and
Interaction of Proteins
Phosphorylation can do more than control a protein’s activity; it can
create docking sites where other proteins can bind, thus promoting the
assembly of proteins into larger complexes. For example, when extracellular signals stimulate a class of cell-surface, transmembrane proteins
called receptor tyrosine kinases, they cause the receptor proteins to phosphorylate themselves on certain tyrosines. The phosphorylated tyrosines
then serve as docking sites for the binding and activation of various
intracellular signaling proteins, which pass along the message to the cell
interior and change the behavior of the cell (see Figure 16–32).
Phosphorylation is not the only form of covalent modification that can
affect a protein’s activity or location. More than 100 types of covalent
modifications can occur in the cell, each playing its own role in regulating protein function. Many proteins are modified by the addition of an
acetyl group to a lysine side chain. And the addition of the fatty acid
palmitate to a cysteine side chain drives a protein to associate with cell
membranes. Attachment of ubiquitin, a 76-amino-acid polypeptide, can
target a protein for degradation, as we discuss in Chapter 7. Each of these
modifying groups is enzymatically added or removed depending on the
needs of the cell.
A large number of proteins are modified on more than one amino acid
side chain. The p53 protein, which plays a central part in controling how
a cell responds to DNA damage and other stresses, can be modified at
20 sites (Figure 4–43). Because an enormous number of combinations of
these 20 modifications is possible, the protein’s behavior can in principle
be altered in a huge number of ways.
The set of covalent modifications that a protein contains at any moment
constitutes an important form of regulation. The attachment or removal
of these modifying groups controls the behavior of a protein, changing its
activity or stability, its binding partners, or its location inside the cell. In
some cases, the modification alters the protein’s conformation; in others,
it serves as a docking site for other proteins to attach. This layer of control enables the cell to make optimal use of its proteins, and it allows the
cell to respond rapidly to changes in its environment.
How Proteins Are Controlled
SOME KNOWN MODIFICATIONS OF PROTEIN p53
C
N
50 amino acids
P
phosphate
Ac
acetyl
U
ubiquitin
GTP-Binding Proteins Are Also Regulated by the Cyclic
Gain and Loss of a Phosphate Group
Eukaryotic cells have a second way to regulate protein activity by phosphate addition and removal. In this case, however, the phosphate is not
enzymatically transferred from ATP to the protein. Instead, the phosphate
is part of a guanine nucleotide—guanosine triphosphate (GTP)—that is
bound tightly to various types of GTP-binding proteins. These proteins
act as molecular switches: they are in their active conformation when
GTP is bound, but they can hydrolyze this GTP to GDP, which releases a
phosphate and flips the proteinECB4
to an
inactive conformation. As with proe4.44/4.42
tein phosphorylation, this process is reversible: the active conformation
is regained by dissociation of the GDP, followed by the binding of a fresh
molecule of GTP (Figure 4–44).
A large variety of such GTP-binding proteins function as molecular
switches in cells. The dissociation of GDP and its replacement by GTP,
which turns the switch on, is often stimulated in response to a signal
received by the cell. The GTP-binding proteins in turn bind to other proteins to control their activities; their crucial role in intracellular signaling
pathways is discussed in detail in Chapter 16.
ATP Hydrolysis Allows Motor Proteins to Produce Directed
Movements in Cells
We have seen how conformational changes in proteins play a central
part in enzyme regulation and cell signaling. But conformational changes
also play another important role in the operation of the eukaryotic cell:
they enable certain specialized proteins to drive directed movements of
cells and their components. These motor proteins generate the forces
responsible for muscle contraction and most other eukaryotic cell movements. They also power the intracellular movements of organelles and
macromolecules. For example, they help move chromosomes to opposite
ends of the cell during mitosis (discussed in Chapter 18), and they move
organelles along cytoskeletal tracks (discussed in Chapter 17).
How are shape changes in proteins used to generate such orderly movements? If, for example, a protein is required to walk along a cytoskeletal
fiber, it can move by undergoing a series of conformational changes.
However, with nothing to drive these changes in an orderly sequence,
the shape changes will be perfectly reversible. Thus the protein can only
wander randomly back and forth (Figure 4–45).
GTP-binding protein
Pi
GTP
GTP
HYDROLYSIS
GDP
GDP
GTP
SLOW
FAST
GTP
ON
OFF
OFF
ON
ACTIVE
INACTIVE
INACTIVE
ACTIVE
155
Figure 4–43 The modification of a
protein at multiple sites can control the
protein’s behavior. This diagram shows
some of the covalent modifications that
control the activity and degradation of the
protein p53, an important gene regulatory
protein that regulates a cell’s response
to damage (discussed in Chapter 18).
Not all of these modifications will be
present at the same time. Colors along
the body of the protein represent distinct
protein domains, including one that binds
to DNA (green) and one that activates
gene transcription (pink). All of the
modifications shown are located within
relatively unstructured regions of the
polypeptide chain.
Question 4–7
Explain how phosphorylation and
the binding of a nucleotide (such as
ATP or GTP) can both be used to
regulate protein activity. What do
you suppose are the advantages of
either form of regulation?
Figure 4–44 GTP-binding proteins
function as molecular switches. A GTPbinding protein requires the presence
of a tightly bound GTP molecule to be
active (switch ON). The active protein can
shut itself off by hydrolyzing its bound
GTP to GDP and inorganic phosphate (Pi),
which converts the protein to an inactive
conformation (switch OFF). To reactivate
the protein, the tightly bound GDP must
dissociate, a slow step that can be greatly
accelerated by specific signals; once the
GDP dissociates, a molecule of GTP quickly
replaces it, returning the protein to its active
conformation.
156
Chapter 4
Protein Structure and Function
Figure 4–45 Changes in conformation can allow a protein to
“walk” along a cytoskeletal filament. This protein’s three different
conformations allow it to wander randomly back and forth while bound
to a filament. Without an input of energy to drive its movement in a
single direction, the protein will only shuffle aimlessly, getting nowhere.
1
To make the conformational changes unidirectional—and force the entire
cycle of movement to proceed in one direction—it is enough to make
any one of the steps irreversible. For most proteins that are able to move
in a single direction for long distances, this irreversibility is achieved
by coupling one of the conformational changes to the hydrolysis of an
ATP molecule bound to the protein—which is why motor proteins are
also ATPases. A great deal of free energy is released when ATP is hydrolyzed, making it very unlikely that the protein will undergo a reverse
shape change—as required for moving backward. (Such a reversal would
require that the ATP hydrolysis be reversed, by adding a phosphate molecule to ADP to form ATP.) As a consequence, the protein moves steadily
forward (Figure 4–46).
2
Many motor proteins generate directional movement by using the
hydrolysis of a tightly bound ATP molecule to drive an orderly series of
conformational changes. These movements can be rapid: the muscle
motor protein myosin walks along actin filaments at about 6 μm/sec during muscle contraction (as discussed in Chapter 17).
3
ECB4 m3.76/4.44
Proteins Often Form Large Complexes That Function as
Protein Machines
1
ATP
BINDING
A
P
P
P
2
ATP HYDROLYSIS
P
A
P
P
3
RELEASE
OF ADP
AND Pi
A P P
ADP
Pi
1
direction of
movement
As one progresses from small, single-domain proteins to large proteins
formed from many domains, the functions that the proteins can perform
become more elaborate. The most complex tasks, however, are carried
out by large protein assemblies formed from many protein molecules.
Now that it is possible to reconstruct biological processes in cell-free systems in a test tube, it is clear that each central process in a cell—including
DNA replication, gene transcription, protein synthesis, vesicle budding,
and transmembrane signaling—is catalyzed by a highly coordinated,
linked set of many proteins. In most such protein machines, the hydrolysis of bound nucleoside triphosphates (ATP or GTP) drives an ordered
series of conformational changes in some of the individual protein subunits, enabling the ensemble of proteins to move coordinately. In this way,
the appropriate enzymes can be positioned to carry out successive reactions in a series—as during the synthesis of proteins on a ribosome, for
example (discussed in Chapter 7). Likewise, a large multiprotein complex
moves rapidly along DNA to replicate the DNA double helix during cell
division (discussed in Chapter 6). A simple mechanical analogy is illustrated in Figure 4–47.
Cells have evolved a large number of different protein machines suited to
performing a variety of biological tasks. Cells employ protein machines
for the same reason that humans have invented mechanical and electronic machines: for almost any job, manipulations that are spatially and
temporally coordinated through linked processes are much more efficient
than is the sequential use of individual tools.
Figure 4–46 A schematic model of how a motor protein uses ATP
hydrolysis to move in one direction along a cytoskeletal filament. An
orderly transition among three conformations is driven by the hydrolysis
of a bound ATP molecule and the release of the products: ADP and
inorganic phosphate (Pi). Because these transitions are coupled to the
hydrolysis of ATP, the entire cycle is essentially irreversible. Through
repeated cycles, the protein moves continuously to the right along
the filament. The movement of a single molecule of myosin has been
captured by atomic force microscopy.
How Proteins Are Studied
Pi ADP
ATP
ATP
ATP
ADP Pi
ATP
ADP + Pi
ADP + Pi
Figure 4–47 “Protein machines” can carry out complex functions. These
machines are made of individual proteins that collaborate to perform a specific
task (Movie 4.11). The movement of these proteins is often coordinated by the
hydrolysis of a bound nucleotide such as ATP. Conformational changes of this type
are especially useful to the cell if they occur in a large protein assembly in which
the activities of several different protein molecules can be coordinated by the
movements within the complex.
How Proteins Are Studied
Understanding how a particular protein functions calls for detailed strucECB4 e4.43/4.46
tural and biochemical analyses—both of which require
large amounts of
pure protein. But isolating a single type of protein from the thousands
of other proteins present in a cell is a formidable task. For many years,
proteins had to be purified directly from the source—the tissues in which
they are most plentiful. That approach was inconvenient, entailing, for
example, early-morning trips to the slaughterhouse. More important, the
complexity of intact tissues and organs is a major disadvantage when
trying to purify particular molecules, because a long series of chromatography steps is generally required. These procedures not only take weeks
to perform, but they also yield only a few milligrams of pure protein.
Nowadays, proteins are more often isolated from cells that are grown in
a laboratory (see, for example, Figure 1–38). Often these cells have been
“tricked” into making large quantities of a given protein using the genetic
engineering techniques that we describe in Chapter 10. Such engineered
cells frequently allow large amounts of pure protein to be obtained in
only a few days.
In this section, we outline how proteins are extracted and purified from
cultured cells and other sources. We describe how these proteins are
analyzed to determine their amino acid sequence and their three-dimensional structure. Finally, we discuss how technical advances are allowing
proteins to be analyzed, cataloged, manipulated, and even designed from
scratch.
Proteins Can be Purified from Cells or Tissues
Whether starting with a piece of liver, a dish of cultured cells, or a vat
of bacterial, yeast, or animal cells that have been engineered to produce a protein of interest, the first step in any purification procedure is
to break open the cells to release their contents. The resulting slurry is
called a cell homogenate or extract. This physical disruption is followed by
an initial fractionation procedure to separate out the class of molecules
of interest—for example, all the soluble proteins in the cell (Panel 4–3,
pp. 164–165).
With this collection of proteins in hand, the job is then to isolate the
desired protein. The standard approach involves purifying the protein
Question 4–8
Explain why the hypothetical
enzymes in Figure 4–47 have a
great advantage in opening the
safe if they work together in a
protein complex, as opposed to
working individually in an unlinked,
sequential manner.
157
158
Chapter 4
Protein Structure and Function
protein X covalently
attached to
column matrix
matrix of
affinity
column
MIXTURE OF
PROTEINS
APPLIED
TO COLUMN
proteins that
bind to protein X
adhere to column
most proteins pass
through the column
ELUTION WITH
HIGH SALT
OR A CHANGE
IN pH
purified X-binding proteins
ECB4 e4.49/4.47
Figure 4–48 Affinity chromatography can be used to isolate the
binding partners of a protein of interest. The purified protein
of interest (protein X) is covalently attached to the matrix of a
chromatography column. An extract containing a mixture of proteins
is then loaded onto the column. Those proteins that associate with
protein X inside the cell will usually bind to it on the column. Proteins
not bound to the column pass right through, and the proteins that are
bound tightly to protein X can then be released by changing the pH or
ionic composition of the washing solution.
through a series of chromatography steps, which use different materials
to separate the individual components of a complex mixture into portions, or fractions, based on the properties of the protein—such as size,
shape, or electrical charge. After each separation step, the fractions are
examined to determine which ones contain the protein of interest. These
fractions are then pooled and subjected to additional chromatography
steps until the desired protein is obtained in pure form.
The most efficient forms of protein chromatography separate polypeptides
on the basis of their ability to bind to a particular molecule—a process
called affinity chromatography (Panel 4–4, p. 166). If large amounts of
antibodies that recognize the protein are available, for example, they can
be attached to the matrix of a chromatography column and used to help
extract the protein from a mixture (see Panel 4–2, pp. 146–147).
Affinity chromatography can also be used to isolate proteins that interact
physically with the protein being studied. In this case, a purified protein
of interest is attached tightly to the column matrix; the proteins that bind
to it will remain in the column and can then be removed by changing the
composition of the washing solution (Figure 4–48).
Proteins can also be separated by electrophoresis. In this technique, a
mixture of proteins is loaded onto a polymer gel and subjected to an
electric field; the polypeptides will then migrate through the gel at different speeds depending on their size and net charge (Panel 4–5, p. 167). If
too many proteins are present in the sample, or if the proteins are very
similar in their migration rate, they can be resolved further using twodimensional gel electrophoresis (see Panel 4–5). These electrophoretic
approaches yield a number of bands or spots that can be visualized by
staining; each band or spot contains a different protein. Chromatography
and electrophoresis—both developed more than 50 years ago but greatly
improved since—have been instrumental in building an understanding
of what proteins look like and how they behave (Table 4–2). Both techniques are still frequently used in laboratories.
Once a protein has been obtained in pure form, it can be used in biochemical assays to study the details of its activity. It can also be subjected
to techniques that reveal its amino acid sequence and precise threedimensional structure.
Determining a Protein’s Structure Begins with
Determining Its Amino Acid Sequence
The task of determining the amino acid sequence of a protein can be
accomplished in several ways. For many years, sequencing a protein was
done by directly analyzing the amino acids in the purified protein. First,
the protein was broken down into smaller pieces using a selective protease; the enzyme trypsin, for example, cleaves polypeptide chains on
the carboxyl side of a lysine or an arginine. Then the identities of the
amino acids in each fragment were determined chemically. The first protein sequenced in this way was the hormone insulin, in 1955.
How Proteins Are Studied
Table 4–2 Historical Landmarks in Our Understanding of Proteins
1838
The name “protein” (from the Greek proteios, “primary”) was suggested by Berzelius for the complex nitrogen-rich
substance found in the cells of all animals and plants.
1819–1904
Most of the 20 common amino acids found in proteins were discovered.
1864
Hoppe-Seyler crystallized, and named, the protein hemoglobin.
1894
Fischer proposed a lock-and-key analogy for enzyme–substrate interactions.
1897
Buchner and Buchner showed that cell-free extracts of yeast can break down sucrose to form carbon dioxide and
ethanol, thereby laying the foundations of enzymology.
1926
Sumner crystallized urease in pure form, demonstrating that proteins could possess the catalytic activity of
enzymes; Svedberg developed the first analytical ultracentrifuge and used it to estimate the correct molecular
weight of hemoglobin.
1933
Tiselius introduced electrophoresis for separating proteins in solution.
1934
Bernal and Crowfoot presented the first detailed X-ray diffraction patterns of a protein, obtained from crystals of
the enzyme pepsin.
1942
Martin and Synge developed chromatography, a technique now widely used to separate proteins.
1951
Pauling and Corey proposed the structure of a helical conformation of a chain of amino acids—the α helix—and the
structure of the β sheet, both of which were later found in many proteins.
1955
Sanger determined the order of amino acids in insulin, the first protein whose amino acid sequence was
determined.
1956
Ingram produced the first protein fingerprints, showing that the difference between sickle-cell hemoglobin and
normal hemoglobin is due to a change in a single amino acid (Movie 4.12).
1960
Kendrew described the first detailed three-dimensional structure of a protein (sperm whale myoglobin) to a
resolution of 0.2 nm, and Perutz proposed a lower-resolution structure for hemoglobin.
1963
Monod, Jacob, and Changeux recognized that many enzymes are regulated through allosteric changes in their
conformation.
1966
Phillips described the three-dimensional structure of lysozyme by X-ray crystallography, the first enzyme to be
analyzed in atomic detail.
1973
Nomura reconstituted a functional bacterial ribosome from purified components.
1975
Henderson and Unwin determined the first three-dimensional structure of a transmembrane protein
(bacteriorhodopsin), using a computer-based reconstruction from electron micrographs.
1976
Neher and Sakmann developed patch-clamp recording to measure the activity of single ion-channel proteins.
1984
Wüthrich used nuclear magnetic resonance (NMR) spectroscopy to solve the three-dimensional structure of a
soluble sperm protein.
1988
Tanaka and Fenn separately developed methods for the analysis of proteins and other biological macromolecules.
1996–2013
Mann, Aebersold, Yates, and others developed efficient methods for using mass spectrometry to identify proteins
in complex mixtures, exploiting the availability of complete genome sequences.
A much faster way to determine the amino acid sequence of proteins that
have been isolated from organisms for which the full genome sequence is
known is a method called mass spectrometry. This technique determines
the exact mass of every peptide fragment in a purified protein, which then
allows the protein to be identified from a database that contains a list of
every protein thought to be encoded by the genome of the organism in
question. Such lists are computed by taking the genome sequence of the
organism and applying the genetic code (discussed in Chapter 7).
To perform mass spectrometry, the peptides derived from digestion with
trypsin are blasted with a laser. This treatment heats the peptides, causing them to become electrically charged (ionized) and ejected in the form
of a gas. Accelerated by a powerful electric field, the peptide ions then fly
toward a detector; the time it takes them to arrive is related to their mass
and their charge. (The larger the peptide is, the more slowly it moves; the
159
160
Chapter 4
Protein Structure and Function
Figure 4–49 Mass spectrometry can be used to identify proteins
by determining the precise masses of peptides derived from
them. As indicated, this in turn allows the proteins to be produced in
the large amounts needed for determining their three-dimensional
structure. In this example, the protein of interest is excised from a
polyacrylamide gel after two-dimensional electrophoresis (see Panel
4–5, p. 167) and then digested with trypsin. The peptide fragments
are loaded into the mass spectrometer, and their exact masses are
measured. Genome sequence databases are then searched to find the
protein encoded by the organism in question whose profile matches
this peptide fingerprint. Mixtures of proteins can also be analyzed in
this way. (Image courtesy of Patrick O’Farrell.)
single protein spot excised from gel
N
C
abundance
PEPTIDES PRODUCED
BY TRYPTIC DIGESTION
HAVE THEIR MASSES
MEASURED USING A
MASS SPECTROMETER
0
m
z (mass to charge ratio)
1600
PROTEINS PREDICTED FROM GENOME
SEQUENCES ARE SEARCHED FOR MATCHES
WITH THEORETICAL MASSES CALCULATED
FOR ALL TRYPSIN-RELEASED PEPTIDES
IDENTIFICATION OF PROTEIN
SUBSEQUENTLY ALLOWS ISOLATION
OF CORRESPONDING GENE
THE GENE SEQUENCE ALLOWS LARGE
AMOUNTS OF THE PROTEIN TO BE OBTAINED
BY GENETIC ENGINEERING TECHNIQUES
ECB4 e4.45/4.48
more highly charged it is, the faster it moves.) The set of exact masses of
the protein fragments produced by trypsin cleavage then serves as a “fingerprint” that identifies the protein—and its corresponding gene—from
publicly accessible databases (Figure 4–49).
This approach can even be applied to complex mixtures of proteins,
for example, starting with an extract containing all the proteins made
by yeast cells grown under a particular set of conditions. To obtain the
increased resolution required to distinguish individual proteins, such
mixtures are frequently analyzed using tandem mass spectrometry. In this
case, after the peptides pass through the first mass spectrometer, they
are broken into even smaller fragments and analyzed by a second mass
spectrometer.
Although all the information required for a polypeptide chain to fold is
contained in its amino acid sequence, we have not yet learned how to
reliably predict a protein’s detailed three-dimensional conformation—the
spatial arrangement of its atoms—from its sequence alone. At present,
the only way to discover the precise folding pattern of any protein is by
experiment, using either X-ray crystallography or nuclear magnetic
resonance (NMR) spectroscopy (How We Know, pp. 162–163).
Genetic Engineering Techniques Permit the Large-Scale
Production, Design, and Analysis of Almost Any Protein
Advances in genetic engineering techniques now permit the production
of large quantities of almost any desired protein. In addition to making
life much easier for biochemists interested in purifying specific proteins,
this ability to churn out huge quantities of a protein has given rise to an
entire biotechnology industry (Figure 4–50). Bacteria, yeast, and cultured
mammalian cells are now used to mass produce a variety of therapeutic
proteins, such as insulin, human growth hormone, and even the fertilityenhancing drugs used to boost egg production in women undergoing in
vitro fertilization. Preparing these proteins previously required the collection and processing of vast amounts of tissue and other biological
products—including, in the case of the fertility drugs, the urine of postmenopausal nuns.
The same sorts of genetic engineering techniques can also be employed
to produce new proteins and enzymes that contain novel structures or
perform unusual tasks: metabolizing toxic wastes, synthesizing lifesaving drugs, or operating under conditions that would destroy most
biological catalysts (see Chapter 3 How We Know, pp. 104–106). Most
of these synthetic catalysts are nowhere near as effective as naturally
occurring enzymes in terms of their ability to speed the rate of selected
chemical reactions. But, as we continue to learn more about how proteins and enzymes exploit their unique conformations to carry out their
biological functions, our ability to make novel proteins with useful functions can only improve.
How Proteins Are Studied
Of course, to be able to study—or benefit from—the activity of an engineered protein in a living organism, the DNA encoding that protein must
somehow be introduced into cells. Again, thanks to genetic engineering
techniques, we are able to do just that. We discuss these methods in great
detail in Chapter 10.
The Relatedness of Proteins Aids the Prediction of Protein
Structure and Function
Biochemists have made enormous progress in understanding the structure and function of proteins over the past 150 years (see Table 4–2,
p. 159). These advances are the fruits of decades of painstaking research
on isolated proteins, performed by individual scientists working tirelessly
on single proteins or protein families, one by one, sometimes for their
entire careers. In the future, however, more and more of these investigations of protein conformation and activity will likely take place on a larger
scale.
Improvements in our ability to rapidly sequence whole genomes, and
the development of methods such as mass spectrometry, have fueled
our ability to determine the amino acid sequences of enormous numbers of proteins. Millions of unique protein sequences from thousands
of different species have thereby been deposited into publicly available databases, and the collection is expected to double in size every
two years. Comparing the amino acid sequences of all of these proteins
reveals that the majority belong to protein families that share specific
“sequence patterns”—stretches of amino acids that fold into distinct
structural domains. In some of these families, the proteins contain only a
single structural domain. In others, the proteins include multiple domains
arranged in novel combinations (Figure 4–51).
Figure 4–50 Biotechnology companies
produce mass quantities of useful
proteins. Shown in this photograph are
the fermenters used to grow the cells
needed for such large-scale protein
production.ECB4
(Courtesy
of Bioengineering
e4.50/4.51
AG, Switzerland.)
Although the number of multidomain families is growing rapidly, the
discovery of novel single domains appears to be leveling off. This plateau suggests that the vast majority of proteins may fold up into a limited
number of structural domains—perhaps as few as 10,000 to 20,000. For
many single-domain families, the structure of at least one family member
is known. And knowing the structure of one family member allows us
to say something about the structure of its relatives. By this account, we
have some structural information for almost three-quarters of the proteins archived in databases (Movie 4.13).
A future goal is to acquire the ability to look at a protein’s amino acid
sequence and be able to deduce its structure and gain insight into its
function. We are coming closer to being able to predict protein structure based on sequence information, but there is still a long way to go.
Predicting how a protein will function, alone, as part of a complex, or as
part of a network in the cell, is much more challenging. But, the closer we
get to addressing these questions, the closer we should be to understanding the fundamental basis of life.
family 1
Figure 4–51 Most proteins belong to structurally related families.
(A) More than two-thirds of all well-studied proteins contain a single
structural domain. The members of these single-domain families
can have different amino acid sequences but fold into a protein
with a similar shape. (B) During evolution, structural domains have
been combined in different ways to produce families of multidomain
proteins. Almost all novelty in protein structure comes from the way
these single domains are arranged. The number of multidomain
families being added to the public databases is still rapidly increasing,
unlike the number of novel single domains.
family 2
(A) single-domain protein families
(B) a two-domain protein family
161
162
How we Know
PROBING PROTEIN STRUCTURE
As you’ve no doubt already concluded in reading this
chapter, for many proteins, their three-dimensional
shape determines their function. So to learn more about
how a protein works, it helps to know exactly what it
looks like.
The problem is that most proteins are too small to be
seen in any detail, even with a powerful electron microscope. To follow the path of an amino acid chain that
is folded into a protein molecule, you need to be able
to “see” its individual atoms. Scientists use two main
methods to map the locations of atoms in a protein.
The first involves the use of X-rays. Like light, X-rays
are a form of electromagnetic radiation. But they have a
wavelength that’s much shorter: 0.1 nanometer (nm) as
opposed to the 400–700 nm wavelength of visible light.
That tiny wavelength—which is the approximate diameter of a hydrogen atom—allows scientists to probe the
structure of very small objects at the atomic level.
A second method, called nuclear magnetic resonance
(NMR) spectroscopy, takes advantage of the fact that—
in many atoms—the nucleus is intrinsically magnetic.
When exposed to a large magnet, these nuclei act like
tiny bar magnets and align themselves with the magnetic field. If they are then excited with a blast of radio
waves, the nuclei will wobble around their magnetic
axes, and, as they relax back into the aligned position,
they will give off a signal that can be used to reveal their
relative positions in a protein.
Using these techniques, investigators have painstakingly
pieced together many thousands of protein structures.
With the help of computer graphics programs, they have
been able to traverse the surfaces and climb inside these
proteins, exploring the nooks where ATP likes to nestle, for example, or examining the loops and helices that
proteins use to grab hold of a ligand or wrap around a
segment of DNA. If the protein happens to belong to a
virus or to a cancer cell, seeing its structure can provide
clues to designing drugs that might thwart an infection
or eliminate a tumor.
X-rays
To determine a protein’s structure using X-ray crystallography, you first need to coax the protein into forming
crystals: large, highly ordered arrays of the pure protein
in which every molecule has the same conformation and
is perfectly aligned with its neighbors. Growing highquality protein crystals is still something of an art and
is largely a matter of trial and error. Although robotic
methods increase efficiency, it can still take years to find
the right conditions—and some proteins resist crystallization altogether.
If you’re lucky enough to get good crystals, you are
ready for the X-ray analysis. When a narrow beam of
X-rays is directed at a protein crystal, the atoms in the
protein molecules scatter the incoming X-rays. These
scattered waves either reinforce or cancel one another,
producing a complex diffraction pattern that is collected
by electronic detectors. The position and intensity
of each spot in the diffraction pattern contains information about the position of the atoms in the protein
crystal (Figure 4–52).
Because these patterns are so complex—even a small
protein can generate 25,000 discrete spots—computers
are used to interpret them and transform them by complex mathematical calculations into maps of the relative
spatial positions of the atoms. By combining information
obtained from such maps with the amino acid sequence
of the protein, you can eventually generate an atomic
model of the protein’s structure. To determine whether
the protein undergoes conformational changes in its
structure when it binds a ligand that boosts its activity,
you might subsequently try crystallizing it in the presence of its ligand. With crystals of sufficient quality, even
small atomic movements can be detected by comparing
the structures obtained in the presence and absence of
stimulatory or inhibitory ligands.
Magnets
The trouble with X-ray crystallography is that you need
crystals. And not all proteins like to form such orderly
assemblies. Many have intrinsically disordered regions
that wiggle around too much to stack neatly into a crystalline array. Others might not crystallize in the absence
of the membranes in which they normally reside.
The other way to solve the structure of a protein does
not require protein crystals. If the protein is small—say,
50,000 daltons or less—you can determine its structure
by NMR spectroscopy. In this technique, a concentrated
solution of pure protein is placed in a strong magnetic
field and then bombarded with radio waves of different
frequencies. Hydrogen nuclei, in particular, will generate an NMR signal that can be used to determine the
distances between these atoms in different parts of the
protein. This information is then used to build a model
of how the hydrogens are arranged in space. Again,
combined with the known amino acid sequence, an
NMR spectrum can allow you to compute the threedimensional structure of the protein (Figure 4–53). If
the protein is larger than 50,000 daltons, you can try to
break it up into its constituent functional domains and
analyze each domain by NMR.
How Proteins Are Studied
163
X-ray diffraction pattern
obtained from the protein crystal
diffracted beams
(B)
protein crystal
beam
stop
X-ray source
(A)
calculation of
structure from
diffraction pattern
beam
of X-rays
(C)
(D)
Figure 4–52 The structure of a protein can be determined by X-ray crystallography. Ribulose bisphosphate carboxylase is an
enzyme that plays a central role in CO2 fixation during photosynthesis. (A) X-ray diffraction apparatus; (B) photograph of crystal;
(C) diffraction pattern; (D) three-dimensional structure determined from the pattern (α helices are shown in green, and β sheets in red ).
(B, courtesy of C. Branden; C, courtesy of J. Hajdu and I. Anderson; D, adapted from original provided by B. Furugren.)
ECB4 e4.46/4.49
Because determining the precise conformation of a protein is so time-consuming and costly—and the resulting
insights so valuable—scientists routinely make their
structures freely available by submitting the information to a publicly accessible database. Thanks to such
databases, anyone interested in viewing the structure
of, say, the ribosome—a complex macromolecular
machine made of several RNAs and more than 50 proteins—can easily do so. In the future, improvements in
(A)
(B)
X-ray crystallography and NMR spectroscopy should
permit rapid analysis of many more proteins and protein machines. And once enough structures have been
determined, it might become possible to generate algorithms for accurately predicting structure solely on the
basis of a protein’s amino acid sequence. After all, it is
the sequence of the amino acids alone that determines
how each protein folds up into its three-dimensional
shape.
Figure 4–53 NMR spectroscopy can be used
to determine the structure of small proteins
or protein domains. (A) Two-dimensional NMR
spectrum derived from the C-terminal domain
of the enzyme cellulase, which breaks down
cellulose. The spots represent interactions between
neighboring hydrogen atoms. (B) The set of
overlapping structures shown all satisfy the distance
constraints equally well. (Courtesy of P. Kraulis.)
164
Panel 4–3
CELL BREAKAGE AND INITIAL FRACTIONATION OF CELL EXTRACTS
BREAKING CELLS AND TISSUES
The first step in the
purification of most
proteins is to disrupt
tissues and cells in a
controlled fashion.
Using gentle mechanical procedures, called homogenization,
the plasma membranes of cells can be ruptured so that the cell
contents are released. Four commonly used procedures are
shown here.
1 Break cells with
high-frequency
sound (ultrasound).
The resulting thick soup (called
a homogenate or an extract)
contains large and small molecules
from the cytosol, such as enzymes,
ribosomes, and metabolites, as well
as all of the membrane-enclosed
organelles.
2 Use a mild detergent
to make holes in the
plasma membrane.
cell
suspension
or
tissue
3 Force cells through
a small hole using
high pressure.
swinging-arm rotor
THE CENTRIFUGE
armored chamber
4 Shear cells between
a close-fitting rotating
plunger and the thick
walls of a glass vessel.
When carefully conducted,
homogenization leaves most
of the membrane-enclosed
organelles largely intact.
centrifugal force
tube
sedimenting material
metal bucket
CENTRIFUGATION
Many cell fractionations are done
in a second type of rotor, a
swinging-arm rotor.
fixedangle
rotor
CELL
HOMOGENATE
before
centrifugation
The metal buckets that hold the tubes are
free to swing outward as the rotor turns.
SUPERNATANT
smaller and less
dense components
CENTRIFUGATION
PELLET
larger and more
dense components
BEFORE
refrigeration
AFTER
vacuum
motor
Centrifugation is the most widely used procedure to separate a
homogenate into different parts, or fractions. The homogenate is
placed in test tubes and rotated at high speed in a centrifuge or
ultracentrifuge. Present-day ultracentrifuges rotate at speeds up
to 100,000 revolutions per minute and produce enormous forces,
as high as 600,000 times gravity.
Such speeds require centrifuge chambers to be refrigerated and
have the air evacuated so that friction does not heat up the
homogenate. The centrifuge is surrounded by thick armor plating,
because an unbalanced rotor can shatter with an explosive release
of energy. A fixed-angle rotor can hold larger volumes than a
swinging-arm rotor, but the pellet forms less evenly, as shown.
ECB4 Panel 4.04a
How Proteins Are Studied
DIFFERENTIAL CENTRIFUGATION
Centrifugation separates cell components on the basis of size and density. The larger
and denser components experience the greatest centrifugal force and move most
rapidly. They sediment to form a pellet at the bottom of the tube, while smaller, less
dense components remain in suspension above, a portion called the supernatant.
Repeated centrifugation at progressively
higher speeds will fractionate cell
homogenates into their components.
LOW-SPEED
CENTRIFUGATION
cell
homogenate
165
SUPERNATANT 1
SUPERNATANT 2
SUPERNATANT 3
MEDIUM-SPEED
CENTRIFUGATION
HIGH-SPEED
CENTRIFUGATION
VERY HIGH-SPEED
CENTRIFUGATION
PELLET 1
PELLET 2
whole cells
nuclei
cytoskeletons
mitochondria
lysosomes
peroxisomes
PELLET 3
closed fragments
of endoplasmic
reticulum
other small vesicles
PELLET 4
ribosomes
viruses
large macromolecules
VELOCITY SEDIMENTATION
sample
CENTRIFUGATION
FRACTIONATION
centrifuge tube pierced
at its base
slowly sedimenting
component
stabilizing
sucrose
gradient
(e.g., 5→20%)
automated rack of small collecting
tubes allows fractions to be collected
as the rack moves from left to right
fast-sedimenting
component
Subcellular components sediment at different rates according to their
size after being carefully layered over a dilute salt solution and then
centrifuged through it. In order to stabilize the sedimenting
components against convective mixing in the tube, the solution contains
a continuous shallow gradient of sucrose that increases in concentration
toward the bottom of the tube. The gradient is typically 5→20%
sucrose. When sedimented through such a dilute sucrose gradient, using
a swinging-arm rotor, different cell components separate into distinct
bands that can be collected individually.
EQUILIBRIUM SEDIMENTATION
The ultracentrifuge can also be used to
separate cell components on the basis of their
buoyant density, independently of their
size or shape. The sample is usually either
layered on top of, or dispersed within, a
steep density gradient that contains a
very high concentration of sucrose or cesium
chloride. Each subcellular component will
move up or down when centrifuged until it
reaches a position where its density matches
its surroundings and then will move no further.
A series of distinct bands will eventually be
produced, with those nearest the bottom of the
tube containing the components of highest
buoyant density. The method is also called
density gradient centrifugation.
rack movement
After an appropriate centrifugation time, the
bands may be collected, most simply by
puncturing the plastic centrifuge tube and
collecting drops from the bottom, as shown here.
At equilibrium, components
have migrated to a region in
the gradient that matches
their own density.
The sample is distributed
throughout the sucrose
density gradient.
CENTRIFUGATION
CENTRIFUGATION
low-buoyant
density
component
sample
high-buoyant
density
component
steep
sucrose
gradient
(e.g., 20→70%)
START
BEFORE EQUILIBRIUM
A sucrose gradient is shown here,
but denser gradients can be formed with
cesium chloride that are particularly useful
for separating nucleic acids (DNA and RNA).
ECB4 Panel 4.04b
EQUILIBRIUM
The final bands can be
collected from the base of
the tube, as shown above for
velocity sedimentation.
Panel 4–4
166
PROTEIN SEPARATION BY CHROMATOGRAPHY
PROTEIN SEPARATION
+
_
+
+
+
_
+
_
+
COLUMN CHROMATOGRAPHY
_
_
_
_
Proteins are often fractionated by column chromatography. A mixture of proteins in
solution is applied to the top of a cylindrical column filled with a permeable solid
matrix immersed in solvent. A large amount of solvent is then pumped through the
column. Because different proteins are retarded to different extents by their
interaction with the matrix, they can be collected separately as they flow out from
the bottom. According to the choice of matrix, proteins can be separated according
to their charge, hydrophobicity, size, or ability to bind to particular chemical
groups (see below ).
sample
applied
+
solvent continuously
applied to the top of
column from a large
reservoir of solvent
Proteins are very diverse. They differ in
size, shape, charge, hydrophobicity, and
their affinity for other molecules. All of
these properties can be exploited to
separate them from one another so
that they can be studied individually.
THREE KINDS OF
CHROMATOGRAPHY
Although the material used to form
the matrix for column chromatography
varies, it is usually packed in the
column in the form of small beads.
A typical protein purification strategy
might employ in turn each of the
three kinds of matrix described
below, with a final protein
purification of up to 10,000-fold.
Purity can easily be assessed by gel
electrophoresis (Panel 4–5).
solvent flow
+
+ + ++
+
+
+
+
+ + +
+
+
+
+
porous
plug
test
tube
time
solvent flow
+ + +
+
+
+
+ +
+ + + +
+
+
+
+
+
+
+
+
+++ +
+
+
+
solid
matrix
positively
charged
bead
+
+
+
small molecules
retarded
free
positively
charged
molecule
(A) ION-EXCHANGE CHROMATOGRAPHY
Ion-exchange columns are packed with
small beads carrying either positive or
negative charges that retard proteins
of the opposite charge. The association
between a protein and the matrix
depends on the pH and ionic strength
of the solution passing down the
column. These can be varied in a
controlled way to achieve an effective
separation.
solvent flow
porous beads
bound
negatively
charged
molecule
large molecules
unretarded
(B) GEL-FILTRATION CHROMATOGRAPHY
Gel-filtration columns separate
proteins according to their size. The
matrix consists of tiny porous beads.
Protein molecules that are small
enough to enter the holes in the beads
are delayed and travel more slowly
through the column. Proteins that
cannot enter the beads are washed out
of the column first. Such columns also
allow an estimate of protein size.
ECB4 Panel 4.05
fractionated molecules
eluted and collected
bead with
covalently
attached
substrate
molecule
bound
enzyme
molecule
other proteins
pass through
(C) AFFINITY CHROMATOGRAPHY
Affinity columns contain a matrix
covalently coupled to a molecule that
interacts specifically with the protein
of interest (e.g., an antibody, or an
enzyme substrate). Proteins that bind
specifically to such a column can
subsequently be released by a pH
change or by concentrated salt
solutions, and they emerge highly
purified (see also Figure 4–48).
Panel 4–5
PROTEIN SEPARATION BY ELECTROPHORESIS
GEL ELECTROPHORESIS
sample loaded onto gel
by pipette
cathode
plastic casing
The detergent
sodium dodecyl
sulfate (SDS)
is used to
solubilize
proteins for SDS
polyacrylamidegel electrophoresis.
167
protein with two
subunits, A and B,
joined by a disulfide
(S–S) bond
CH3
CH2
CH2
A
CH2
single-subunit
protein
B
C
S-S
CH2
CH2
CH2
HEATED WITH SDS AND MERCAPTOETHANOL
CH2
_
__ __ _ __
__
___ ___ ___ __
__ ___
___ _ _ _ __ _____ ___ __ _ _ _
__ _ _ __
_ _
_
_ _ __ __ _SH__ ____ __ __ _ _ ___ _ _ _ _ _ ___
_
_
_
_
_
_
_
__
__ ___ __
__ _ _ ___ __
_ _ __
__
_ _
_____ __
__ _ ___ _HS
_
__ _ _ _ ___
_
_
__ _ _ _
_____ __ _ _ ___ ___ ___ negatively
__ _ _ _ _ ___ _
_ _ ___ __
_
C
_ charged SDS
_ _ __
_ _ __
molecules
A
B
CH2
buffer
CH2
+ anode
gel
CH2
CH2
O
O
buffer
O
ISOELECTRIC FOCUSING
For any protein there is a characteristic
pH, called the isoelectric point, at which
the protein has no net charge and
therefore will not move in an electric
field. In isoelectric focusing, proteins
are electrophoresed in a narrow tube of
polyacrylamide gel in which a pH
gradient is established by a mixture of
special buffers. Each protein moves to a
point in the pH gradient that corresponds
to its isoelectric point and stays there.
stable pH gradient
9
8
7
6
5
4
At low pH,
the protein
is positively
charged.
At high pH,
the protein
is negatively
charged.
++ _
+_ _+
+
+
_+_
+_ _+
+
_+_
+_ _+
+
+
__
_+ _
__+
+
+++
+
+
+++
___
_
_
___
The protein shown here has an isoelectric pH of 6.5.
O
POLYACRYLAMIDE-GEL ELECTROPHORESIS
Na +
SDS
SDS polyacrylamide-gel electrophoresis
B
(SDS-PAGE)
Individual polypeptide chains form a complex with
C
negatively charged molecules of sodium dodecyl
sulfate (SDS) and therefore migrate as negatively
charged SDS–protein complexes through a slab of
A
porous polyacrylamide gel. The apparatus used for
this electrophoresis technique is shown above (left ).
A reducing agent (mercaptoethanol) is usually added
to break any –S–S– linkages within or between
proteins. Under these conditions, unfolded polypeptide
chains migrate at a rate that reflects their molecular
weight.
+
slab of polyacrylamide gel
TWO-DIMENSIONAL POLYACRYLAMIDE-GEL ELECTROPHORESIS
Complex mixtures of proteins cannot be resolved well on one-dimensional gels, but
two-dimensional gel electrophoresis, combining two different separation methods, can
be used to resolve more than 1000 proteins in a two-dimensional protein map. In the
first step, native proteins are separated in a narrow gel on the basis of their intrinsic
charge using isoelectric focusing (see left ). In the second step, this gel is placed on top of
a gel slab, and the proteins are subjected to SDS-PAGE (see above ) in a direction
perpendicular to that used in the first step. Each protein migrates to form a discrete spot.
All the proteins in
an E. coli bacterial
cell are separated
in this twodimensional gel, in
which each spot
corresponds to a
different
polypeptide chain.
They are separated
according to their
isoelectric point
from left to right
and to their
molecular weight
from top to
bottom. (Courtesy
of Patrick O'Farrell.)
basic
SDS migration (mol. wt. x 10–3)
When an electric field is applied to a solution
containing protein molecules, the molecules
will migrate in a direction and at a speed that
reflects their size and net charge. This forms
the basis of the technique called
electrophoresis.
10
S
100
50
25
stable pH gradient
acidic
168
Chapter 4
Protein Structure and Function
Essential Concepts
•
Living cells contain an enormously diverse set of protein molecules,
each made as a linear chain of amino acids linked together by covalent peptide bonds.
•
Each type of protein has a unique amino acid sequence, which determines both its three-dimensional shape and its biological activity.
•
The folded structure of a protein is stabilized by multiple noncovalent
interactions between different parts of the polypeptide chain.
•
Hydrogen bonds between neighboring regions of the polypeptide
backbone often give rise to regular folding patterns, known as α helices and β sheets.
•
The structure of many proteins can be subdivided into smaller globular regions of compact three-dimensional structure, known as protein
domains.
•
The biological function of a protein depends on the detailed chemical
properties of its surface and how it binds to other molecules, called
ligands.
•
When a protein catalyzes the formation or breakage of a specific
covalent bond in a ligand, the protein is called an enzyme and the
ligand is called a substrate.
•
At the active site of an enzyme, the amino acid side chains of the
folded protein are precisely positioned so that they favor the formation of the high-energy transition states that the substrates must
pass through to be converted to product.
•
The three-dimensional structure of many proteins has evolved so
that the binding of a small ligand can induce a significant change in
protein shape.
•
Most enzymes are allosteric proteins that can exist in two conformations that differ in catalytic activity, and the enzyme can be turned
on or off by ligands that bind to a distinct regulatory site to stabilize
either the active or the inactive conformation.
•
The activities of most enzymes within the cell are strictly regulated.
One of the most common forms of regulation is feedback inhibition,
in which an enzyme early in a metabolic pathway is inhibited by the
binding of one of the pathway’s end products.
•
Many thousands of proteins in a typical eukaryotic cell are regulated
by cycles of phosphorylation and dephosphorylation.
•
GTP-binding proteins also regulate protein function in eukaryotes;
they act as molecular switches that are active when GTP is bound
and inactive when GDP is bound; turning themselves off by hydrolyzing their bound GTP to GDP.
•
Motor proteins produce directed movement in eukaryotic cells
through conformational changes linked to the hydrolysis of ATP to
ADP.
•
Highly efficient protein machines are formed by assemblies of allosteric proteins in which the various conformational changes are
coordinated to perform complex functions.
•
Covalent modifications added to a protein’s amino acid side chains
can control the location and function of the protein and can serve as
docking sites for other proteins.
•
Starting from crude cell or tissue homogenates, individual proteins
can be obtained in pure form by using a series of chromatography
steps.
•
The function of a purified protein can be discovered by biochemical
analyses, and its exact three-dimensional structure can be determined by X-ray crystallography or NMR spectroscopy.
Chapter 4 End-of-Chapter Questions
169
Key terms
active site
mass spectrometry
allosteric
motor protein
α helixN-terminus
amino acid sequence
nuclear magnetic resonance
antibody
(NMR) spectroscopy
antigen
peptide bond
β sheet
polypeptide, polypeptide chain
binding site
polypeptide backbone
C-terminus
primary structure
chromatography
protein
coiled-coil
protein domain
conformation
protein family
disulfide bond
protein kinase
electrophoresis
protein machine
enzyme
protein phosphatase
feedback inhibition
protein phosphorylation
fibrous protein
quaternary structure
globular protein
secondary structure
GTP-binding protein
side chain
helix
substrate
intrinsically disordered
subunit
sequence
tertiary structure
ligand
transition state
lysozyme
X-ray crystallography
Questions
Question 4–9
Look at the models of the protein in Figure 4–12. Is the
red α helix right- or left-handed? Are the three strands that
form the large β sheet parallel or antiparallel? Starting at
the N-terminus (the purple end), trace your finger along the
peptide backbone. Are there any knots? Why, or why not?
Question 4–10
Which of the following statements are correct? Explain your
answers.
A. The active site of an enzyme usually occupies only a
small fraction of the enzyme surface.
B.Catalysis by some enzymes involves the formation of
a covalent bond between an amino acid side chain and a
substrate molecule.
H.Affinity chromatography separates molecules according
to their intrinsic charge.
I.Upon centrifugation of a cell homogenate, smaller
organelles experience less friction and thereby sediment
faster than larger ones.
Question 4–11
What common feature of α helices and β sheets makes them
universal building blocks for proteins?
Question 4–12
Protein structure is determined solely by a protein’s amino
acid sequence. Should a genetically engineered protein in
which the original order of all amino acids is reversed have
the same structure as the original protein?
C.A β sheet can contain up to five strands, but no more.
Question 4–13
D. The specificity of an antibody molecule is contained
exclusively in loops on the surface of the folded light-chain
domain.
Consider the following protein sequence as an α helix:
Leu-Lys-Arg-Ile-Val-Asp-Ile-Leu-Ser-Arg-Leu-Phe-Lys-Val.
How many turns does this helix make? Do you find anything
remarkable about the arrangement of the amino acids in
this sequence when folded into an α helix? (Hint: consult the
properties of the amino acids in Figure 4–3.)
E. The possible linear arrangements of amino acids are so
vast that new proteins almost never evolve by alteration of
old ones.
F.Allosteric enzymes have two or more binding sites.
Question 4–14
G.Noncovalent bonds are too weak to influence the threedimensional structure of macromolecules.
Simple enzyme reactions often conform to the equation
E+S
ES → EP
E+P
170
Chapter 4
Protein Structure and Function
where E, S, and P are enzyme, substrate, and product,
respectively.
A. What does ES represent in this equation?
B. Why is the first step shown with bidirectional arrows and
the second step as a unidirectional arrow?
C. Why does E appear at both ends of the equation?
D.One often finds that high concentrations of P inhibit the
enzyme. Suggest why this might occur.
E.If compound X resembles S and binds to the active site
of the enzyme but cannot undergo the reaction catalyzed
by it, what effects would you expect the addition of X to
the reaction to have? Compare the effects of X and of the
accumulation of P.
Question 4–19
A motor protein moves along protein filaments in the cell.
Why are the elements shown in the illustration not sufficient
to mediate directed movement (Figure Q4–19)? With
reference to Figure 4–46, modify the illustration shown
here to include other elements that are required to create a
unidirectional motor, and justify each modification you make
to the illustration.
Figure Q4–19
Question 4–15
Which of the following amino acids would you expect
to find more often near the center of a folded globular
protein? Which ones would you expect to find more often
exposed to the outside? Explain your answers. Ser, Ser-P (a
Ser residue that is phosphorylated), Leu, Lys, Gln, His, Phe,
Val, Ile, Met, Cys–S–S–Cys (two cysteines that are disulfidebonded), and Glu. Where would you expect to find the most
N-terminal amino acid and the most C-terminal amino acid?
Question 4–20
Gel-filtration chromatography separates molecules
according to their size (see Panel 4–4, p. 166). Smaller
ECB4 inQ4.18/Q4.18
molecules diffuse faster
solution than larger ones, yet
smaller molecules migrate more slowly through a gelfiltration column than larger ones. Explain this paradox.
What should happen at very rapid flow rates?
Question 4–16
Question 4–21
Assume you want to make and study fragments of a protein.
Would you expect that any fragment of the polypeptide
chain would fold the same way as it would in the intact
protein? Consider the protein shown in Figure 4–19. Which
fragments do you suppose are most likely to fold correctly?
As shown in Figure 4–16, both α helices and the coiled-coil
structures that can form from them are helical structures,
but do they have the same handedness in the figure?
Explain why?
Question 4–17
How is it possible for a change in a single amino acid in a
protein of 1000 amino acids to destroy its function, even
when that amino acid is far away from any ligand-binding
site?
Neurofilament proteins assemble into long, intermediate
filaments (discussed in Chapter 17), found in abundance
running along the length of nerve cell axons. The C-terminal
region of these proteins is an unstructured polypeptide,
hundreds of amino acids long and heavily modified by the
addition of phosphate groups. The term “polymer brush”
has been applied to this part of the neurofilament. Can you
suggest why?
Question 4–18
An enzyme isolated from a mutant bacterium grown at
20°C works in a test tube at 20°C but not at 37°C (37°C is
the temperature of the gut, where this bacterium normally
lives). Furthermore, once the enzyme has been exposed
to the higher temperature, it no longer works at the lower
one. The same enzyme isolated from the normal bacterium
works at both temperatures. Can you suggest what happens
(at the molecular level) to the mutant enzyme as the
temperature increases?
Question 4–22
chapter five
5
DNA and Chromosomes
Life depends on the ability of cells to store, retrieve, and translate the
genetic instructions required to make and maintain a living organism.
This hereditary information is passed on from a cell to its daughter cells
at cell division, and from generation to generation in multicellular organisms through the reproductive cells—eggs and sperm. These instructions
are stored within every living cell in its genes—the information-containing elements that determine the characteristics of a species as a whole
and of the individuals within it.
At the beginning of the twentieth century, when genetics emerged as
a science, scientists became intrigued by the chemical nature of genes.
The information in genes is copied and transmitted from cell to daughter
cells millions of times during the life of a multicellular organism, and it
survives the process essentially unchanged. What kind of molecule could
be capable of such accurate and almost unlimited replication, and also be
able to direct the development of an organism and the daily life of a cell?
What kind of instructions does the genetic information contain? How are
these instructions physically organized so that the enormous amount of
information required for the development and maintenance of even the
simplest organism can be contained within the tiny space of a cell?
The answers to some of these questions began to emerge in the 1940s,
when it was discovered from studies in simple fungi that genetic information consists primarily of instructions for making proteins. Proteins
perform most of the cell’s functions: they serve as building blocks for
cell structures; they form the enzymes that catalyze the cell’s chemical
reactions; they regulate the activity of genes; and they enable cells to
The STRUCTURE OF DNA
The Structure of
Eukaryotic Chromosomes
The Regulation of
Chromosome Structure
172
Chapter 5
DNA and Chromosomes
move and to communicate with one another. With hindsight, it is hard
to imagine what other type of instructions the genetic information could
have contained.
The other crucial advance made in the 1940s was the recognition that
deoxyribonucleic acid (DNA) was the likely carrier of this genetic information. But the mechanism whereby the hereditary information is copied for
transmission from one generation of cells to the next, and how proteins
are specified by the instructions in DNA, remained completely mysterious
until 1953, when the structure of DNA was determined by James Watson
and Francis Crick. The structure immediately revealed how DNA might be
copied, or replicated, and it provided the first clues about how a molecule
of DNA might encode the instructions for making proteins. Today, the fact
that DNA is the genetic material is so fundamental to our understanding
of life that it is difficult to appreciate what an enormous intellectual gap
this discovery filled.
In this chapter, we begin by describing the structure of DNA. We see how,
despite its chemical simplicity, the structure and chemical properties of
DNA make it ideally suited for carrying genetic information. The genes of
every cell on Earth are made of DNA, and insights into the relationship
between DNA and genes have come from experiments in a wide variety
of organisms. We then consider how genes and other important segments
of DNA are arranged in the single, long DNA molecule that forms the core
of each chromosome in the cell. Finally, we discuss how eukaryotic cells
fold these long DNA molecules into compact chromosomes inside the
nucleus. This packing has to be done in an orderly fashion so that the
chromosomes can be duplicated and apportioned correctly between the
two daughter cells at each cell division. It must also allow the DNA to be
accessed by the proteins that replicate and repair DNA, and regulate the
activity of its many genes.
(A)
dividing cell
nondividing cell
(B)
10 μm
Figure 5–1 Chromosomes become visible
as eukaryotic cells prepare to divide.
(A) Two adjacent plant cells photographed
in a fluorescence microscope. The DNA
is labeled with a fluorescent dye (DAPI)
that binds to it. The DNA is packaged
into chromosomes,
which become visible
ECB4 e5.01/5.01
as distinct structures only when they
condense in preparation for cell division,
as shown on the left. The cell on the
right, which is not dividing, contains the
identical chromosomes, but they cannot be
distinguished as individual entities because
the DNA is in a much more extended
conformation at this phase in the cell’s life
cycle. (B) Schematic diagram of the outlines
of the two cells and their chromosomes.
(A, courtesy of Peter Shaw.)
This is the first of five chapters that deal with basic genetic mechanisms—
the ways in which the cell maintains and makes use of the genetic
information carried in its DNA. In Chapter 6, we discuss the mechanisms
by which the cell accurately replicates and repairs its DNA. In Chapter 7,
we consider gene expression—how genes are used to produce RNA and
protein molecules. In Chapter 8, we describe how a cell controls gene
expression to ensure that each of the many thousands of proteins encoded
in its DNA is manufactured at the proper time and place. In Chapter 9, we
discuss how present-day genes evolved from distant ancestors, and, in
Chapter 10, we consider some of the experimental techniques used to
study both DNA and its role in fundamental cell processes.
An enormous amount has been learned about these subjects in the past
60 years. Much less obvious, but equally important, is that our knowledge
is very incomplete; thus a great deal still remains to be discovered about
how DNA provides the instructions to build living things.
The Structure of DNA
Well before biologists understood the structure of DNA, they had recognized that inherited traits and the genes that determine them were
associated with the chromosomes. Chromosomes (named from the
Greek chroma, “color,” because of their staining properties) were discovered in the nineteenth century as threadlike structures in the nucleus of
eukaryotic cells that become visible as the cells begin to divide (Figure
5–1). As biochemical analysis became possible, researchers learned that
chromosomes contain both DNA and protein. But which of these components encoded the organism’s genetic information was not clear.
The Structure of DNA
173
We now know that the DNA carries the hereditary information of the
cell and that the protein components of chromosomes function largely to
package and control the enormously long DNA molecules. But biologists
in the 1940s had difficulty accepting DNA as the genetic material because
of the apparent simplicity of its chemistry (see How We Know, pp. 174–
176). DNA, after all, is simply a long polymer composed of only four types
of nucleotide subunits, which are chemically very similar to one another.
Then, early in the 1950s, DNA was examined by X-ray diffraction analysis, a technique for determining the three-dimensional atomic structure
of a molecule (see Figure 4–52). The early results indicated that DNA
is composed of two strands wound into a helix. The observation that
DNA is double-stranded was of crucial significance. It provided one of
the major clues that led, in 1953, to a correct model for the structure
of DNA. This structure immediately suggested how DNA could encode
the instructions necessary for life, and how these instructions could be
copied and passed along when cells divide. In this section, we examine
the structure of DNA and explain in general terms how it is able to store
hereditary information.
A DNA Molecule Consists of Two Complementary Chains
of Nucleotides
A molecule of deoxyribonucleic acid (DNA) consists of two long polynucleotide chains. Each chain, or strand, is composed of four types of
nucleotide subunits, and the two strands are held together by hydrogen
bonds between the base portions of the nucleotides (Figure 5–2).
(A)
building blocks of DNA
(B)
DNA strand
sugar
phosphate
+
sugarphosphate
(C)
5′
G
base
(guanine)
A
DNA double helix
3′
5′
G
A
T
A
T
G
C
G
T
A
G
sugar–phosphate
backbone
C
C
G
C
G
A
A
T
G
C
C
A
A
T
A
A
C
C
C
G
T
T
G
5′
(D)
5′
C
T
A
nucleotide
double-stranded DNA
3′
3′
C
G
G
3′
hydrogen-bonded
base pairs
3′
G
T
5′
Figure 5–2 DNA is made of four
nucleotide building blocks. (A) Each
nucleotide is composed of a sugar–
phosphate covalently linked to a
base—guanine (G) in this figure. (B) The
nucleotides are covalently linked together
into polynucleotide chains, with a sugar–
phosphate backbone from which the bases
(A, C, G, and T) extend. (C) A DNA molecule
is composed of two polynucleotide chains
(DNA strands) held together by hydrogen
bonds between the paired bases. The
arrows on the DNA strands indicate the
polarities of the two strands, which run
antiparallel to each other in the DNA
molecule. (D) Although the DNA is shown
straightened out in (C), in reality, it is wound
into a double helix, as shown here.
174
How we Know
GENES ARE MADE OF DNA
By the 1920s, scientists generally agreed that genes
reside on chromosomes, and they knew that chromosomes are composed of both DNA and proteins. But
because DNA is so chemically simple, they naturally
assumed that genes had to be made of proteins, which
are much more chemically diverse than DNA molecules.
Even when the experimental evidence suggested otherwise, this assumption proved hard to shake.
Messages from the dead
The case for DNA began to emerge in the late 1920s,
when a British medical officer named Fred Griffith made
an astonishing discovery. He was studying Streptococcus
pneumoniae (pneumococcus), a bacterium that causes
pneumonia. As antibiotics had not yet been discovered,
infection with this organism was usually fatal. When
living S strain of
S. pneumoniae
mouse dies
of infection
living R strain of
S. pneumoniae
mouse lives
S strain
heat-killed
mouse lives
living R strain
+
mouse dies
of infection
S strain
heat-killed
living, pathogenic
S strain recovered
Figure 5–3 Griffith showed that
heat-killed, infectious bacteria can
transform harmless, living bacteria
into pathogenic ones. The bacterium
Streptococcus pneumoniae comes in two
forms that differ from one another in their
microscopic appearance and in their ability
to cause disease. Cells of the pathogenic
strain, which are lethal when injected into
mice, are encased in a slimy, glistening
polysaccharide capsule. When grown on
a plate of nutrients in the laboratory, this
disease-causing bacterium forms colonies
that look dome-shaped and smooth;
hence it is designated the S form. The
harmless strain of the pneumococcus,
on the other hand, lacks this protective
coat; it forms colonies that appear flat
and rough—hence, it is referred to as the
R form. As illustrated, Griffith found that
a substance present in the pathogenic
S strain could permanently change, or
transform, the nonlethal R strain into the
deadly S strain.
The Structure of DNA
grown in the laboratory, pneumococci come in two
forms: a pathogenic form that causes a lethal infection
when injected into animals, and a harmless form that is
easily conquered by the animal’s immune system and
does not produce an infection.
In the course of his investigations, Griffith injected various preparations of these bacteria into mice. He showed
that pathogenic pneumococci that had been killed by
heating were no longer able to cause infection. The
surprise came when Griffith injected both heat-killed
pathogenic bacteria and live harmless bacteria into the
same mouse. This combination proved lethal: not only
did the animals die of pneumonia, but Griffith found that
their blood was teeming with live bacteria of the pathogenic form (Figure 5–3). The heat-killed pneumococci
had somehow converted the harmless bacteria into the
lethal form. What’s more, Griffith found that the change
was permanent: he could grow these “transformed” bacteria in culture, and they remained pathogenic. But what
was this mysterious material that turned harmless bacteria into killers? And how was this change passed on to
progeny bacteria?
Transformation
175
S-strain cells
fractionation of a cell-free
extract into classes of
molecules
RNA
protein
DNA
lipid carbohydrate
molecules tested for transformation of R-strain cells
R
strain
R
strain
S
strain
R
strain
R
strain
CONCLUSION: The molecule that
carries the heritable information
is DNA.
Figure 5–4 Avery, MacLeod, and McCarty demonstrated
that DNA is the genetic material. The researchers prepared
an extract from the disease-causing S strain of pneumococci
and showed that the “transforming principle” that would
permanently change the harmless R-strain pneumococci into the
pathogenic S strain is DNA. This was the first evidence that DNA
could serve as the genetic material.
Griffith’s remarkable finding set the stage for the experiments that would provide the first strong evidence that
genes are made of DNA. The American bacteriologist
Oswald Avery, following up on Griffith’s work, discovered
that the harmless pneumococcus could be transformed
into a pathogenic strain in a culture tube by exposing
it to an extract prepared from the pathogenic strain. It
would take another 15 years, however, for Avery and
his colleagues Colin MacLeod and Maclyn McCarty to
successfully purify the “transforming principle” from
this soluble extract and to demonstrate that the active
ingredient was DNA. Because the transforming principle
caused a heritable change in the bacteria that received
it, DNA must be the very stuff of which genes are made.
ECB4 e5.04/5.04
characteristic of DNA; furthermore, they showed that
enzymes that destroy proteins and RNA did not affect
the ability of the extract to transform bacteria, while
enzymes that destroy DNA inactivated it. And like
Griffith before them, the investigators found that their
purified preparation changed the bacteria permanently:
DNA from the pathogenic species was taken up by the
harmless species, and this change was faithfully passed
on to subsequent generations of bacteria.
The 15-year delay was in part a reflection of the academic climate—and the widespread supposition that
the genetic material was likely to be made of protein.
Because of the potential ramifications of their work, the
researchers wanted to be absolutely certain that the
transforming principle was DNA before they announced
their findings. As Avery noted in a letter to his brother,
also a bacteriologist, “It’s lots of fun to blow bubbles,
but it’s wiser to prick them yourself before someone else
tries to.” So the researchers subjected the transforming material to a battery of chemical tests (Figure 5–4).
They found that it exhibited all the chemical properties
This landmark study offered rigorous proof that purified
DNA can act as genetic material. But the resulting paper,
published in 1944, drew remarkably little attention.
Despite the meticulous care with which these experiments were performed, geneticists were not immediately
convinced that DNA is the hereditary material. Many
argued that the transformation might have been caused
by some trace protein contaminant in the preparations.
Or that the extract might contain a mutagen that alters
the genetic material of the harmless bacteria—converting them to the pathogenic form—rather than containing
the genetic material itself.
176
Chapter 5
DNA and Chromosomes
Virus cocktails
The debate was not settled definitively until 1952, when
Alfred Hershey and Martha Chase fired up their laboratory blender and demonstrated, once and for all, that
genes are made of DNA. The researchers were studying T2—a virus that infects and eventually destroys the
bacterium E. coli. These bacteria-killing viruses behave
like little molecular syringes: they inject their genetic
material into the bacterial host cell, while the empty
virus heads remain attached outside (Figure 5–5A).
Once inside the bacterial cell, the viral genes direct the
formation of new virus particles. In less than an hour,
the infected cells explode, spewing thousands of new
viruses into the medium. These then infect neighboring
bacteria, and the process begins again.
The beauty of T2 is that these viruses contain only two
kinds of molecules: DNA and protein. So the genetic
material had to be one or the other. But which? The
experiment was fairly straightforward. Because the
viral DNA enters the bacterial cell, while the rest of the
virus particle remains outside, the researchers decided
to radioactively label the protein in one batch of virus
and the DNA in another. Then, all they had to do was
follow the radioactivity to see whether viral DNA or
viral protein wound up inside the bacteria. To do this,
Hershey and Chase incubated their radiolabeled viruses
with E. coli; after allowing a few minutes for infection to
take place, they poured the mix into a Waring blender
and hit “puree.” The blender’s spinning blades sheared
the empty virus heads from the surfaces of the bacterial cells. The researchers then centrifuged the sample
to separate the heavier, infected bacteria, which formed
a pellet at the bottom of the centrifuge tube, from the
empty viral coats, which remained in suspension (Figure
5–5B).
As you have probably guessed, Hershey and Chase
found that the radioactive DNA entered the bacterial
cells, while the radioactive proteins remained outside
with the empty virus heads. They found that the radioactive DNA was also incorporated into the next generation
of virus particles.
This experiment demonstrated conclusively that viral
DNA enters bacterial host cells, whereas viral protein
does not. Thus, the genetic material in this virus had
to be made of DNA. Together with the studies done by
Avery, MacLeod, and McCarty, this evidence clinched
the case for DNA as the agent of heredity.
E. coli
(A)
(B)
virus
E. coli
cell
DNA labeled
with 32P
genetic material:
protein or DNA?
CENTRIFUGE
protein labeled
with 35S
viruses allowed to
infect E. coli
viral heads
sheared off
the bacteria
infected bacteria
contain 32P but
not 35S
Figure 5–5 Hershey and Chase showed definitively that genes are made of DNA. (A) The researchers worked with T2 viruses, which
are made entirely of protein and DNA. Each virus acts as a molecular syringe, injecting its genetic material into a bacterium; the empty
viral capsule remains attached to the outside of the cell. (B) To determine whether the genetic material of the virus is protein or DNA,
the researchers radioactively labeled the DNA in one batch of viruses with 32P and the proteins in a second batch of viruses with 35S.
Because DNA lacks sulfur and the proteins lack phosphorus, these radioactive isotopes provided a handy way for the researchers to
distinguish these two types of molecules. These labeled viruses were allowed to infect and replicate inside E. coli, and the mixture was
ECB4 e5.05/5.05
then disrupted by brief pulsing in a Waring blender and separated
to part the infected bacteria from the empty viral heads. When the
researchers measured the radioactivity, they found that much of the 32P-labeled DNA had entered the bacterial cells, while the vast
majority of the 35S-labeled proteins remained in solution with the spent viral particles.
177
The Structure of DNA
As we saw in Chapter 2 (Panel 2–6, pp. 76–77), nucleotides are composed of a nitrogen-containing base and a five-carbon sugar, to which
is attached one or more phosphate groups. For the nucleotides in DNA,
the sugar is deoxyribose (hence the name deoxyribonucleic acid), and the
base can be either adenine (A), cytosine (C), guanine (G), or thymine (T). The
nucleotides are covalently linked together in a chain through the sugars
and phosphates, which thus form a backbone of alternating sugar–phosphate–sugar–phosphate (see Figure 5–2B). Because it is only the base that
differs in each of the four types of subunits, each polynucleotide chain
in DNA can be thought of as a necklace: a sugar–phosphate backbone
strung with four types of beads (the four bases A, C, G, and T). These
same symbols (A, C, G, and T) are also commonly used to denote the
four different nucleotides—that is, the bases with their attached sugar
phosphates.
Figure 5–6 The two strands of the
DNA double helix are held together by
hydrogen bonds between complementary
base pairs. (A) The shapes and chemical
structure of the bases allow hydrogen
bonds to form efficiently only between A
and T and between G and C, where atoms
that are able to form hydrogen bonds (see
Panel 2–2, pp. 68–69) can be brought close
together without perturbing the double
helix. Two hydrogen bonds form between
A and T, whereas three form between
G and C. The bases can pair in this way
only if the two polynucleotide chains that
contain them are antiparallel—that is,
oriented in opposite directions. (B) A short
section of the double helix viewed from
its side. Four base pairs are shown. The
nucleotides are linked together covalently
by phosphodiester bonds through the
3’-hydroxyl (–OH) group of one sugar
and the 5’-phosphate (–OPO3) of the
next (see Panel 2–6, pp. 76–77, to review
how the carbon atoms in the sugar ring
are numbered). This linkage gives each
polynucleotide strand a chemical polarity;
that is, its two ends are chemically different.
The 3’ end carries an unlinked –OH group
attached to the 3’ position on the sugar
ring; the 5’ end carries a free phosphate
group attached to the 5’ position on the
sugar ring.
The way in which the nucleotide subunits are linked together gives a
DNA strand a chemical polarity. If we imagine that each nucleotide has a
knob (the phosphate) and a hole (see Figure 5–2A), each strand, formed
by interlocking knobs with holes, will have all of its subunits lined up
in the same orientation. Moreover, the two ends of the strand can be
easily distinguished, as one will have a hole (the 3’ hydroxyl) and the
other a knob (the 5’ phosphate). This polarity in a DNA strand is indicated
by referring to one end as the 3’ end and the other as the 5’ end. This
convention is based on the details of the chemical linkage between the
nucleotide subunits.
The two polynucleotide chains in the DNA double helix are held together
by hydrogen-bonding between the bases on the different strands. All the
bases are therefore on the inside of the double helix, with the sugar–phosphate backbones on the outside (see Figure 5–2D). The bases do not pair
at random, however: A always pairs with T, and G always pairs with C
(Figure 5–6). In each case, a bulkier two-ring base (a purine, see Panel 2–6,
pp. 76–77) is paired with a single-ring base (a pyrimidine). Each purine–
pyrimidine pair is called a base pair, and this complementary base-pairing
enables the base pairs to be packed in the energetically most favorable
3′
5′
5′ end
H
N
N
C
C
H
C
A
C
N
H
C
H
bases
C
O
CH3
O
_
O
H
G
C
C
N
guanine
O
N
H
C
N
C
C
O
H
hydrogen
bond
1 nm
N
H
O
P O
O
O P
_
O O
N
C
C
C
H
O
_
O P O
_
O
C
H
cytosine
HO
_
thymine
N
O
C
_
P
O
O
O
O
P O
_
O O
3′ end
H
H
(A)
T
N
H
N
3′
H
C
N
sugar–
phosphate
backbone
C
N
_
O
N
C
C
adenine
N
O
5′
5′ end
(B)
O
O
P O
O
O
G
O
C
O
O
G
O
O
T
G
O
C
O
_
O
sugar
A
O
P
O
OH
hydrogen bond
3′ end
O_
P O
O
phosphodiester
bond
178
Chapter 5
DNA and Chromosomes
Figure 5–7 A space-filling model shows the conformation of the
DNA double helix. The two DNA strands wind around each other to
form a right-handed helix (see Figure 4–14) with 10 bases per turn.
Shown here are 1.5 turns of the DNA double helix. The coiling of the
two strands around each other creates two grooves in the double
helix. The wider groove is called the major groove and the smaller
one the minor groove. The colors of the atoms are: N, blue; O, red;
P, yellow; and H, white.
major
groove
minor
groove
2 nm
arrangement in the interior of the double helix. In this arrangement, each
base pair has a similar width, thus holding the sugar–phosphate backbones an equal distance apart along the DNA molecule. The members
of each base pair can fit together within the double helix because the
two strands of the helix run antiparallel to each other—that is, they are
oriented with opposite polarities (see Figure 5–2C and D). The antiparallel
sugar–phosphate strands then twist around each other to form a double
helix containing 10 base pairs per helical turn (Figure 5–7). This twisting
also contributes to the energetically favorable conformation of the DNA
double helix.
A consequence of the base-pairing requirements is that each strand of
a DNA double helix contains a sequence of nucleotides that is exactly
complementary to the nucleotide sequence of its partner strand—an A
always matches a T on the opposite strand, and a C always matches a
G. This complementarity is of crucial importance when it comes to both
copying and repairing the DNA, as we discuss in Chapter 6. An animated
version of the DNA structure can be seen in Movie 5.1.
The Structure of DNA Provides a Mechanism for Heredity
ECB4
Question 5–1
e5.07/5.07
Which of the following statements
are correct? Explain your answers.
A. A DNA strand has a polarity
because its two ends contain
different bases.
B. G-C base pairs are more stable
than A-T base pairs.
The need for genes to encode information that must be copied and transmitted accurately when a cell divides raised two fundamental questions:
how can the information for specifying an organism be carried in chemical
form, and how can the information be accurately copied? The discovery of the structure of the DNA double helix was a landmark in biology
because it immediately suggested the answers—and thereby resolved the
problem of heredity at the molecular level. In this chapter, we outline the
answer to the first question; in the next chapter, we address in detail the
answer to the second.
Information is encoded in the order, or sequence, of the nucleotides along
each DNA strand. Each base—A, C, T, or G—can be considered a letter in
a four-letter alphabet that is used to spell out biological messages (Figure
5–8). Organisms differ from one another because their respective DNA
molecules have different nucleotide sequences and, consequently, carry
different biological messages. But how is the nucleotide alphabet used to
make up messages, and what do they spell out?
(E) TTCGAGCGACCTAACCTATAG
It had already been established some time before the structure of DNA
was determined that genes contain the instructions for producing proteins. DNA messages, therefore, must somehow be able to encode
proteins. Consideration of the chemical character of proteins makes the
problem easier to define. As discussed in Chapter 4, the function of a protein is determined by its three-dimensional structure, and this structure in
turn is determined by the sequence of the amino acids in its polypeptide
chain. The linear sequence of nucleotides in a gene must therefore be
able to spell out the linear sequence of amino acids in a protein.
Figure 5–8 Linear messages come in
many forms. The languages shown are
(A) English, (B) a musical score, (C) Morse
code, (D) Chinese, and (E) DNA.
The exact correspondence between the 4-letter nucleotide alphabet of
DNA and the 20-letter amino acid alphabet of proteins—the genetic
code—is not obvious from the structure of the DNA molecule, and it took
more than a decade after the discovery of the double helix to work it
(A)
molecular biology is...
(B)
(C)
(D)
ECB4 e5.08/5.08
The Structure of Eukaryotic Chromosomes
Figure 5–9 Most genes contain information to make proteins. As
we discuss in Chapter 7, each protein-coding gene is used to produce
RNA molecules, which then direct the production of the specific
protein molecules.
out. In Chapter 7, we describe this code in detail when we discuss gene
expression—the process by which the nucleotide sequence of a gene is
transcribed into the nucleotide sequence of an RNA molecule, which, in
most cases, is then translated into the amino acid sequence of a protein
(Figure 5–9).
The amount of information in an organism’s DNA is staggering: written out in the four-letter nucleotide alphabet, the nucleotide sequence of
a very small protein-coding gene from humans occupies a quarter of a
page of text, while the complete human DNA sequence would fill more
than 1000 books the size of this one. Herein lies a problem that affects the
architecture of all eukaryotic chromosomes: how can all this information
be packed neatly into every cell nucleus? In the remainder of this chapter,
we discuss the answer to this question.
The Structure of Eukaryotic
Chromosomes
Large amounts of DNA are required to encode all the information needed
to make even a single-celled bacterium, and far more DNA is needed to
encode the information to make a multicellular organism like you. Each
human cell contains about 2 meters (m) of DNA; yet the cell nucleus is
only 5–8 μm in diameter. Tucking all this material into such a small space
is the equivalent of trying to fold 40 km (24 miles) of extremely fine thread
into a tennis ball.
In eukaryotic cells, very long double-stranded DNA molecules are packaged into chromosomes. These DNA molecules not only fit readily inside
the nucleus, but, after they are replicated, they can be easily apportioned
between the two daughter cells at each cell division. The complex task of
packaging DNA is accomplished by specialized proteins that bind to and
fold the DNA, generating a series of coils and loops that provide increasingly higher levels of organization and prevent the DNA from becoming
a tangled, unmanageable mess. Amazingly, the DNA is compacted in a
way that allows it to remain accessible to all of the enzymes and other
proteins that replicate it, repair it, and control the expression of its genes.
Bacteria typically carry their genes on a single, circular DNA molecule.
This molecule is also associated with proteins that condense the DNA,
but these proteins differ from the ones that package eukaryotic DNA.
Although this prokaryotic DNA is called a bacterial “chromosome,” it
does not have the same structure as eukaryotic chromosomes, and less is
known about how it is packaged. Our discussion of chromosome structure
in this chapter will therefore focus entirely on eukaryotic chromosomes.
Eukaryotic DNA Is Packaged into Multiple Chromosomes
In eukaryotes, such as ourselves, the DNA in the nucleus is distributed
among a set of different chromosomes. The DNA in a human nucleus,
for example, contains approximately 3.2 × 109 nucleotides parceled out
into 23 or 24 different types of chromosome (males, with their Y chromosome, have an extra type of chromosome that females do not have). Each
chromosome consists of a single, enormously long, linear DNA molecule
associated with proteins that fold and pack the fine thread of DNA into
a more compact structure. The complex of DNA and protein is called
chromatin. In addition to the proteins involved in packaging the DNA,
gene A
gene B
gene C
RNA A
RNA B
RNA C
179
DNA
double
helix
protein A protein B protein C
ECB4 e5.09/5.09
GENE
EXPRESSION
180
Chapter 5
DNA and Chromosomes
Figure 5–10 Each human chromosome
can be “painted” a different color to
allow its unambiguous identification. The
chromosomes shown here were isolated
from a cell undergoing nuclear division
(mitosis) and are therefore in a highly
compact (condensed) state. Chromosome
painting is carried out by exposing the
chromosomes to a collection of human
DNA molecules that have been coupled
to a combination of fluorescent dyes. For
example, DNA molecules derived from
Chromosome 1 are labeled with one specific
dye combination, those from Chromosome
2 with another, and so on. Because the
labeled DNA can form base pairs (hybridize)
only to its chromosome of origin (discussed
in Chapter 10), each chromosome is
differently colored. For such experiments,
the chromosomes are treated so that the
individual strands of the double-helical DNA
molecules partly separate to enable basepairing with the labeled, single-stranded
DNA, while keeping the chromosome
structure relatively intact. (A) Micrograph
shows the array of chromosomes as they
originally spilled from the lysed cell.
(B) The same chromosomes have been
artificially lined up in order. In this so-called
karyotype, the homologous chromosomes
are numbered and arranged in pairs; the
presence of a Y chromosome reveals that
these chromosomes came from a male.
(From E. Schröck et al., Science 273:494–
497, 1996. With permission from the AAAS.)
1
(A)
2
3
6
7
8
13
14
15
19
20
9
21
4
5
10
11
12
16
17
18
22
(B)
X Y
10 μm
chromosomes are also associated with many other proteins involved in
DNA replication, DNA repair, and gene expression.
With the exception of the germ cells (sperm and eggs) and highly specialized cells that lack DNA entirely (such as mature red blood cells),
human cells each contain
copies of each chromosome, one inherited
ECB4 two
e5.10/5.10
from the mother and one from the father. The maternal and paternal
chromosomes of a pair are called homologous chromosomes (homologs).
The only nonhomologous chromosome pairs are the sex chromosomes
in males, where a Y chromosome is inherited from the father and an
X chromosome from the mother. (Females inherit one X chromosome
from each parent and have no Y chromosome.)
In addition to being different sizes, the different human chromosomes
can be distinguished from one another by a variety of techniques. Each
chromosome can be “painted” a different color using sets of chromosome-specific DNA molecules coupled to different fluorescent dyes
(Figure 5–10). This involves a technique called DNA hybridization, which
takes advantage of complementary base-pairing, as we will describe in
detail in Chapter 10. A more traditional way of distinguishing one chromosome from another is to stain the chromosomes with dyes that bind to
certain types of DNA sequences. These dyes mainly distinguish between
DNA that is rich in A-T nucleotide pairs and DNA that is G-C rich, and
they produce a predictable pattern of bands along each type of chromosome. The patterns that result allow each chromosome to be identified
and numbered.
An ordered display of the full set of 46 human chromosomes is called
the human karyotype (see Figure 5–10). If parts of a chromosome are
lost, or switched between chromosomes, these changes can be detected.
Cytogeneticists analyze karyotypes to detect chromosomal abnormalities
that are associated with some inherited defects (Figure 5–11) and with
certain types of cancer.
Chromosomes Contain Long Strings of Genes
The most important function of chromosomes is to carry the genes—the
functional units of heredity (Figure 5–12). A gene is often defined as a
(A)
(B)
Figure 5–11 Abnormal chromosomes are associated with some
inherited genetic defects. (A) A pair of Chromosomes 12 from
a patient with inherited ataxia, a genetic disease of the brain
characterized by progressive deterioration of motor skills. The
patient has one normal Chromosome 12 (left) and one abnormally
long Chromosome 12, which contains a piece of Chromosome 4 as
identified by its banding pattern. (B) This interpretation was confirmed
by chromosome painting, in which Chromosome 12 was painted blue
and Chromosome 4 was painted red. (From E. Schröck et al., Science
273:494–497, 1996. With permission from the AAAS.)
181
The Structure of Eukaryotic Chromosomes
0.5% of the DNA of the yeast genome
5′
3′
10,000 nucleotide pairs
genes
3′
5′
Figure 5–12 Genes are arranged along chromosomes. This figure shows a small region of the DNA double
helix in one chromosome from the budding yeast S. cerevisiae. The S. cerevisiae genome contains about 12
million nucleotide pairs and 6600 genes—spread across 16 chromosomes. Note that, in each gene, only one of
the two DNA strands actually encodes the information to make an RNA molecule, and this can be either strand, as
indicated by the light red bars. However, a gene is generally denoted to contain both the “coding strand” and its
complement, as in Figure 5–9. The high density of genes is characteristic of S. cerevisiae.
segment of DNA that contains the instructions forECB4
making
a particular
e5.13/5.12
protein or RNA molecule. Most of the RNA molecules encoded by genes
are subsequently used to produce a protein (see Figure 5–9). In some
cases, however, the RNA molecule is the final product; like proteins,
these RNA molecules have diverse functions in the cell, including structural, catalytic, and gene regulatory roles, as we discuss in later chapters.
Together, the total genetic information carried by all the chromosomes in a cell or organism constitutes its genome. Complete genome
sequences have been determined for thousands of organisms, from
E. coli to humans. As might be expected, some correlation exists between
the complexity of an organism and the number of genes in its genome.
For example, the total number of genes ranges from less than 500 for a
simple bacterium to about 30,000 for humans. Bacteria and some single-celled eukaryotes, including S. cerevisiae, have especially compact
genomes: the DNA molecules that make up their chromosomes are little
more than strings of closely packed genes (see Figure 5–12). However,
chromosomes from many eukaryotes—including humans—contain, in
addition to genes and the specific nucleotide sequences required for normal gene expression, a large excess of interspersed DNA. This extra DNA
is sometimes called “junk DNA,” because the usefulness to the cell has
not yet been demonstrated. Although the particular nucleotide sequence
of most of this DNA might not be important, the DNA itself—acting as
spacer material—may be crucial for the long-term evolution of the species and for the proper activity of the genes. In addition, comparisons of
the genome sequences from many different species reveal that a portion
of this extra DNA is highly conserved among related species, indicating
that it serves an important function—although we don’t yet know what
that is.
In general, the more complex an organism, the larger is its genome.
But this relationship does not always hold true. The human genome, for
example, is 200 times larger than that of the yeast S. cerevisiae, but 30
times smaller than that of some plants and at least 60 times smaller than
some species of amoeba (see Figure 1–40). Furthermore, how the DNA is
apportioned over chromosomes also differs from one species to another.
Humans have a total of 46 chromosomes (including both maternal and
paternal sets), but a species of small deer has only 7, while some carp
species have more than 100. Even closely related species with similar
genome sizes can have very different numbers and sizes of chromosomes (Figure 5–13). Thus, although gene number is roughly correlated
with species complexity, there is no simple relationship between gene
number, chromosome number, and total genome size. The genomes and
chromosomes of modern species have each been shaped by a unique history of seemingly random genetic events, acted on by specific selection
pressures, as we discuss in Chapter 9.
182
Chapter 5
DNA and Chromosomes
Y2 X Y1
X Y
Chinese muntjac
Figure 5–13 Two closely related species
can have similar genome sizes but very
different chromosome numbers. In the
evolution of the Indian muntjac deer,
chromosomes that were initially separate,
and that remain separate in the Chinese
species, fused without having a major effect
on the number of genes—or the animal.
(Courtesy of Deborah Carreno, Natural
Wonders Photography.)
Indian muntjac
Specialized DNA Sequences Are Required for DNA
Replication and Chromosome Segregation
To form a functional chromosome, a DNA molecule must do more than
simply carry genes: it must be able to be replicated, and the replicated
copies must be separated and partitioned equally and reliably into the
two daughter cells at each cell division. These processes occur through
ECB4 e5.14/5.13
an ordered series of events, known collectively as the cell cycle. This
cycle of cell growth and division is briefly summarized in Figure 5–14 and
will be discussed in detail in Chapter 18. Only two broad stages of the cell
cycle need concern us in this chapter: interphase, when chromosomes
are duplicated, and mitosis, when they are distributed, or segregated, to
the two daughter nuclei.
During interphase, the chromosomes are extended as long, thin, tangled threads of DNA in the nucleus and cannot be easily distinguished
in the light microscope (see Figure 5–1). We refer to chromosomes in
this extended state as interphase chromosomes. As we discuss in Chapter
6, specialized DNA sequences found in all eukaryotes ensure that DNA
replication occurs efficiently during interphase. One type of nucleotide
sequence acts as a replication origin, where replication of the DNA
begins; eukaryotic chromosomes contain many replication origins to
ensure that the long DNA molecules are replicated rapidly (Figure 5–15).
Another DNA sequence forms the telomeres at each of the two ends of a
chromosome. Telomeres contain repeated nucleotide sequences that are
required for the ends of chromosomes to be replicated. They also cap the
ends of the DNA molecule, preventing them from being mistaken by the
cell as broken DNA in need of repair.
mitotic
spindle
nuclear envelope
surrounding the nucleus
GENE EXPRESSION
AND CHROMOSOME
DUPLICATION
MITOSIS
interphase
chromosome
CELL
DIVISION
mitotic
chromosome
INTERPHASE
M PHASE
INTERPHASE
Figure 5–14 The duplication and segregation of chromosomes occurs through an ordered cell cycle in proliferating cells. During
interphase, the cell expresses many of its genes, and—during part of this phase—it duplicates chromosomes. Once chromosome
duplication is complete, the cell can enter M phase, during which nuclear division, or mitosis, occurs. In mitosis, the duplicated
chromosomes condense, gene expression largely ceases, the nuclear envelope breaks down, and the mitotic spindle forms from
microtubules and other proteins. The condensed chromosomes are then captured by the mitotic spindle, one complete set is pulled
to each end of the cell, and a nuclear envelope forms around each chromosome set. In the final step of M phase, the cell divides to
produce two daughter cells. Only two different chromosomes are shown here for simplicity.
ECB4 e5.15/5.14
The Structure of Eukaryotic Chromosomes
INTERPHASE
M PHASE
INTERPHASE
telomere
replication
origin
CELL
DIVISION
+
centromere
portion of
mitotic spindle
duplicated
chromosomes
in separate cells
183
Figure 5–15 Three DNA sequence
elements are needed to produce a
eucaryotic chromosome that can be
replicated and then segregated at
mitosis. Each chromosome has multiple
origins of replication, one centromere, and
two telomeres. The sequence of events
that a typical chromosome follows during
the cell cycle is shown schematically. The
DNA replicates in interphase, beginning at
the origins of replication and proceeding
bidirectionally from the origins across the
chromosome. In M phase, the centromere
attaches the duplicated chromosomes
to the mitotic spindle so that one copy is
distributed to each daughter cell when
the cell divides. Prior to cell division, the
centromere also helps to hold the compact,
duplicated chromosomes together
until they are ready to be pulled apart.
Telomeres, which form special caps at
the tips of each chromosome, aid in the
replication of chromosome ends.
Eukaryotic chromosomes also contain a third type of specialized DNA
sequence, called the centromere, that allows duplicated chromosomes
to be separated during M phase (see
Figure
5–15). During this stage of
ECB4
e5.16/5.15
the cell cycle, the DNA coils up, adopting a more and more compact
structure, ultimately forming highly compacted, or condensed, mitotic
chromosomes. This is the state in which the duplicated chromosomes can
be most easily visualized (Figure 5–16 and see Figures 5–1 and 5–14).
Once the chromosomes have condensed, the centromere attaches the
mitotic spindle to each duplicated chromosome in a way that allows one
copy of each chromosome to be segregated to each daughter cell (see
Figure 5–15B). We describe the central role that centromeres play in cell
division in Chapter 18.
Interphase Chromosomes Are Not Randomly Distributed
Within the Nucleus
Inside the nucleus, the interphase chromosomes—although longer and
finer than mitotic chromosomes—are nonetheless organized in various
duplicated
chromosome
centromere
(A)
1 μm
chromatid
(B)
Figure 5–16 A typical duplicated mitotic
chromosome is highly compact. Because
DNA is replicated during interphase, each
duplicated mitotic chromosome contains
two identical daughter DNA molecules (see
Figure 5–15A). Each of these very long
DNA molecules, with its associated
proteins, is called a chromatid; once
the two sister chromatids separate, they
are considered individual chromosomes.
(A) A scanning electron micrograph of a
mitotic chromosome. The two chromatids
are tightly joined together. The constricted
region reveals the position of the
centromere. (B) A cartoon representation
of a mitotic chromosome. (A, courtesy of
Terry D. Allen.)
184
Chapter 5
DNA and Chromosomes
Figure 5–17 Interphase chromosomes
occupy their own distinct territories
within the nucleus. DNA probes coupled
with different fluorescent markers were used
to paint individual interphase chromosomes
in a human cell. Viewed in a fluorescence
microscope, each interphase chromosome
is seen to occupy its own discrete territory
within the nucleus, rather than being mixed
with the other chromosomes like spaghetti
in a bowl. Note that pairs of homologous
chromosomes, such as the two copies of
Chromosome 9 indicated, are not generally
located in the same position. (From
M.R. Speicher and N.P. Carter, Nat. Rev.
Genet. 6:782–792, 2005. With permission
from Macmillan Publishers Ltd.)
Chromosome 9
interphase cell
nuclear
envelope
nucleus
10 μm
ways. First, each chromosome tends to occupy a particular region of
the interphase nucleus, and so different chromosomes do not become
extensively entangled with one another (Figure 5–17). In addition, some
ECB4toe5.18/5.17
chromosomes are attached
particular sites on the nuclear envelope—
the pair of concentric membranes that surround the nucleus—or to the
underlying nuclear lamina, the protein meshwork that supports the envelope (discussed in Chapter 17).
The most obvious example of chromosome organization in the interphase nucleus is the nucleolus (Figure 5–18). The nucleolus is where
the parts of the different chromosomes carrying genes that encode ribosomal RNAs cluster together. Here, ribosomal RNAs are synthesized and
combine with proteins to form ribosomes, the cell’s protein-synthesizing
machines. As we discuss in Chapter 7, ribosomal RNAs play both structural and catalytic roles in the ribosome.
The DNA in Chromosomes Is Always Highly Condensed
As we have seen, all eukaryotic cells, whether in interphase or mitosis, package their DNA tightly into chromosomes. Human Chromosome
22, for example, contains about 48 million nucleotide pairs; stretched
out end-to-end, its DNA would extend about 1.5 cm. Yet, during mitosis, Chromosome 22 measures only about 2 μm in length—that is, nearly
10,000 times more compact than the DNA would be if it were stretched
to its full length. This remarkable feat of compression is performed by
proteins that coil and fold the DNA into higher and higher levels of organization. The DNA of interphase chromosomes, although about 20 times
less condensed than that of mitotic chromosomes (Figure 5–19), is still
packed tightly.
Figure 5–18 The nucleolus is the most
prominent structure in the interphase
nucleus. Electron micrograph of a thin
section through the nucleus of a human
fibroblast. The nucleus is surrounded by the
nuclear envelope. Inside the nucleus, the
chromatin appears as a diffuse speckled
mass, with regions that are especially dense,
called heterochromatin (dark staining).
Heterochromatin contains few genes and
is located mainly around the periphery of
the nucleus, immediately under the nuclear
envelope. The large dark region is the
nucleolus, which contains the genes for
ribosomal RNAs; these genes are located
on multiple chromosomes but are clustered
together in the nucleolus. (Courtesy of
E.G. Jordan and J. McGovern.)
nuclear
envelope
heterochromatin
nucleolus
2 μm
The Structure of Eukaryotic Chromosomes
185
In the next sections, we introduce the specialized proteins that make this
compression possible. Bear in mind, though, that chromosome structure
is dynamic. Not only do chromosomes condense and decondense during the cell cycle, but chromosome packaging must be flexible enough
to allow rapid, on-demand access to different regions of the interphase
chromosome, unpacking enough to allow protein complexes access
to specific, localized DNA sequences for replication, repair, or gene
expression.
Nucleosomes Are the Basic Units of Eukaryotic
Chromosome Structure
The proteins that bind to DNA to form eukaryotic chromosomes are traditionally divided into two general classes: the histones and the nonhistone
chromosomal proteins. Histones are present in enormous quantities (more
than 60 million molecules of several different types in each cell), and their
total mass in chromosomes is about equal to that of the DNA itself. The
complex of both classes of protein with nuclear DNA is called chromatin.
Histones are responsible for the first and most fundamental level of chromatin packing, the nucleosome, which was discovered in 1974. When
interphase nuclei are broken open very gently and their contents examined with an electron microscope, much of the chromatin is in the form
of chromatin fibers with a diameter of about 30 nm (Figure 5–20A). If this
chromatin is subjected to treatments that cause it to unfold partially, it
can then be seen in the electron microscope as a series of “beads on a
string” (Figure 5–20B). The string is DNA, and each bead is a nucleosome
core particle, which consists of DNA wound around a core of proteins
formed from histones.
The structure of the nucleosome core particle was determined after first
isolating nucleosomes by treating chromatin in its unfolded, “beads on a
string” form with enzymes called nucleases, which break down DNA by
cutting the phosphodiester bonds between nucleotides. After digestion
for a short period, only the exposed DNA between the core particles—
the linker DNA—is degraded, allowing the core particles to be isolated.
An individual nucleosome core particle consists of a complex of eight
histone proteins—two molecules each of histones H2A, H2B, H3, and
H4—and a stretch of double-stranded DNA, 147 nucleotide pairs long,
that winds around this histone octamer (Figure 5–21). The high-resolution
structure of the nucleosome core particle was solved in 1997, revealing
in atomic detail the disc-shaped histone octamer around which the DNA
is tightly wrapped, making 1.7 turns in a left-handed coil (Figure 5–22).
(A)
interphase
chromatin
5 μm
mitotic chromosome
(B)
Figure 5–19 DNA in interphase
chromosomes is less compact than in
mitotic chromosomes. (A) An electron
micrograph showing an enormous tangle of
chromatin (DNA with its associated proteins)
ECB4 e5.20/5.19
spilling out of a lysed interphase nucleus.
(B) Schematic drawing of a human mitotic
chromosome drawn to the same scale.
(Courtesy of Victoria Foe.)
(A)
(B)
50 nm
Figure 5–20 Nucleosomes can be seen in
the electron microscope. (A) Chromatin
isolated directly from an interphase nucleus
appears in the electron microscope as
a chromatin fiber about 30-nm thick;
a part of one such fiber is shown here.
(B) This electron micrograph shows a
length of a chromatin fiber that has been
experimentally unpacked, or decondensed,
after isolation to show the “beads-on-astring” appearance of the nucleosomes.
(A, courtesy of Barbara Hamkalo;
B, courtesy of Victoria Foe.)
186
Chapter 5
DNA and Chromosomes
linker DNA
“beads-on-a-string”
form of chromatin
core histones
of nucleosome
nucleosome includes
~200 nucleotide
pairs of DNA
NUCLEASE
DIGESTS
LINKER DNA
released
nucleosome
core particle
The linker DNA between each nucleosome core particle can vary in
length from a few nucleotide pairs up to about 80. (The term nucleosome
technically refers to a nucleosome core particle plus one of its adjacent
DNA linkers, as shown in Figure 5–21, but it is often used to refer to the
nucleosome core particle itself.) The formation of nucleosomes converts
a DNA molecule into a chromatin thread that is approximately one-third
the length of the initial piece of DNA, and it provides the first level of DNA
packing.
11 nm
All four of the histones that make up the octamer are relatively small
proteins, with a high proportion of positively charged amino acids (lysine
and arginine). The positive charges help the histones bind tightly to the
negatively charged sugar–phosphate backbone of DNA. These numerous electrostatic interactions explain in part why DNA of virtually any
sequence can bind to a histone octamer. Each of the histones in the
DISSOCIATION
WITH HIGH
CONCENTRATION
OF SALT
histone
octamer
Figure 5–21 Nucleosomes contain DNA wrapped around a protein
core of eight histone molecules. In a test tube, the nucleosome core
particle can be released from chromatin by digestion of the linker DNA
with a nuclease, which degrades the exposed DNA but not the DNA
wound tightly around the nucleosome core. The DNA around each
isolated nucleosome core particle can then be released and its length
determined. With 147 nucleotide pairs in each fragment, the DNA
wraps almost twice around each histone octamer.
147-nucleotide-pair
DNA double helix
viewed
from here
DISSOCIATION
viewed
from here
H2A
H2B
H3
H4
an H3
histone tail
ECB4 e5.22/5.21
DNA double helix
histone H2A
histone H2B
histone H3
histone H4
Figure 5–22 The structure of the nucleosome core particle, as determined by
X-ray diffraction analysis, reveals how DNA is tightly wrapped around a
disc-shaped histone octamer. Two views of a nucleosome core particle are shown
here. The two strands of the DNA double helix are shown in gray. A portion of an
H3 histone tail (green) can be seen extending from the nucleosome core particle,
but the tails of the other histones have been truncated. (Reprinted by permission
ECB4 e5.23/5.22
from K. Luger et al., Nature 389:251–260,
1997. With permission from Macmillan
Publishers Ltd.)
The Structure of Eukaryotic Chromosomes
187
octamer also has a long, unstructured N-terminal amino acid “tail” that
extends out from the nucleosome core particle (see Figure 5–22). These
histone tails are subject to several types of reversible, covalent chemical
modifications that control many aspects of chromatin structure.
The histones that form the nucleosome core are among the most highly
conserved of all known eukaryotic proteins: there are only two differences between the amino acid sequences of histone H4 from peas and
cows, for example. This extreme evolutionary conservation reflects the
vital role of histones in controlling eukaryotic chromosome structure.
Chromosome Packing Occurs on Multiple Levels
Although long strings of nucleosomes form on most chromosomal DNA,
chromatin in the living cell rarely adopts the extended beads-on-a-string
form seen in Figure 5–20B. Instead, the nucleosomes are further packed
on top of one another to generate a more compact structure, such as the
chromatin fiber shown in Figure 5–20A and Movie 5.2. This additional
packing of nucleosomes into a chromatin fiber depends on a fifth histone called histone H1, which is thought to pull adjacent nucleosomes
together into a regular repeating array. This “linker” histone changes the
path the DNA takes as it exits the nucleosome core, allowing it to form a
more condensed chromatin fiber (Figure 5–23).
We saw earlier that during mitosis chromatin becomes so highly condensed that individual chromosomes can be seen in the light microscope.
How is a chromatin fiber folded to produce mitotic chromosomes? The
answer is not yet known in detail, but it is known that the chromatin fiber
is folded into a series of loops, and that these loops are further condensed
to produce the interphase chromosome; finally, this compact string of
loops is thought to undergo at least one more level of packing to form the
mitotic chromosome (Figure 5–24 and Figure 5–25).
C
N
histone H1
Figure 5–23 A linker histone helps to pull
nucleosomes together and pack them
into a more compact chromatin fiber.
Histone H1 consists of a globular region
plus a pair of long tails at its C-terminal
ECB4 e5.24/5.23
and N-terminal ends. The globular region
constrains an additional 20 base pairs of the
DNA where it exits from the nucleosome
core, an activity that is thought to be
important for the formation of the chromatin
fiber. The long C-terminal tail is required for
H1 to bind to chromatin. The positions of
the C-terminal and N-terminal tails in the
nucleosome are not known.
Question 5–2
short region of
DNA double helix
2 nm
11 nm
“beads-on-a-string”
form of chromatin
chromatin fiber
of packed
nucleosomes
30 nm
chromatin fiber
folded into loops
700 nm
Assuming that the histone
octamer (shown in Figure 5–21)
forms a cylinder 9 nm in diameter
and 5 nm in height and that the
human genome forms 32 million
nucleosomes, what volume of
the nucleus (6 μm in diameter) is
occupied by histone octamers?
(Volume of a cylinder is πr2h; volume
of a sphere is 4/3 πr3.) What fraction
of the total volume of the nucleus
do the histone octamers occupy?
How does this compare with the
volume of the nucleus occupied by
human DNA?
centromere
entire
mitotic
chromosome
1400 nm
NET RESULT: EACH DNA MOLECULE HAS BEEN
PACKAGED INTO A MITOTIC CHROMOSOME THAT
IS 10,000-FOLD SHORTER THAN ITS FULLY
EXTENDED LENGTH
Figure 5–24 DNA packing occurs on
several levels in chromosomes. This
schematic drawing shows some of the levels
thought to give rise to the highly condensed
mitotic chromosome. The actual structures
are still uncertain.
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Chapter 5
DNA and Chromosomes
Figure 5–25 The mitotic chromosome contains chromatin that
is packed especially tightly. This scanning electron micrograph
shows a region near one end of a typical mitotic chromosome. Each
knoblike projection is believed to represent the tip of a separate loop
of chromatin. The chromosome has duplicated, forming two sister
chromatids that are still held close together (see Figure 5–16). The
ends of the two chromatids can be distinguished on the right of the
photo. (From M.P. Marsden and U.K. Laemmli, Cell 17:849–858, 1989.
With permission from Elsevier.)
chromatid 1
chromatid 2
The Regulation of Chromosome
Structure
0.1 μm
ECB4 e5.26/5.25
Question 5–3
Histone proteins are among the
most highly conserved proteins in
eukaryotes. Histone H4 proteins
from a pea and a cow, for example,
differ in only 2 of 102 amino acids.
Comparison of the gene sequences
shows many more differences, but
only two change the amino acid
sequence. These observations
indicate that mutations that change
amino acids must have been
selected against during evolution.
Why do you suppose that aminoacid-altering mutations in histone
genes are deleterious?
So far, we have discussed how DNA is packed tightly into chromatin. We
now turn to the question of how this packaging can be regulated to allow
rapid access to the underlying DNA. The DNA in cells carries enormous
amounts of coded information, and cells must be able to get to this information as needed.
In this section, we discuss how a cell can alter its chromatin structure
to expose localized regions of DNA and allow access to specific proteins
and protein complexes, particularly those involved in gene expression
and in DNA replication and repair. We then discuss how chromatin structure is established and maintained—and how a cell can pass on some
forms of this structure to its descendants. The regulation and inheritance
of chromatin structure play crucial parts in the development of eukaryotic organisms.
Changes in Nucleosome Structure Allow Access to DNA
Eukaryotic cells have several ways to adjust the local structure of their
chromatin rapidly. One way takes advantage of chromatin-remodeling
complexes, protein machines that use the energy of ATP hydrolysis to
change the position of the DNA wrapped around nucleosomes (Figure
5–26A). The complexes, which attach to both the histone octamer and
the DNA wrapped around it, can locally alter the arrangement of nucleosomes on the DNA, making the DNA either more accessible (Figure
5–26B) or less accessible to other proteins in the cell. During mitosis,
many of the chromatin-remodeling complexes are inactivated, which
may help mitotic chromosomes maintain their tightly packed structure.
Another way of altering chromatin structure relies on the reversible
chemical modification of the histones. The tails of all four of the core
histones are particularly subject to these covalent modifications (Figure
5–27A). For example, acetyl, phosphate, or methyl groups can be added
to and removed from the tails by enzymes that reside in the nucleus
(Figure 5–27B). These and other modifications can have important consequences for the stability of the chromatin fiber. Acetylation of lysines,
for instance, can reduce the affinity of the tails for adjacent nucleosomes,
thereby loosening chromatin structure and allowing access to particular
nuclear proteins.
Most importantly, however, these modifications can serve as docking
sites on the histone tails for a variety of regulatory proteins. Different
patterns of modifications attract different proteins to particular stretches
of chromatin. Some of these proteins promote chromatin condensation,
whereas others decondense chromatin and facilitate access to the DNA.
Specific combinations of tail modifications and the proteins that bind to
them have different meanings for the cell: one pattern, for example, indicates that a particular stretch of chromatin has been newly replicated;
The Regulation of Chromosome Structure
Figure 5–26 Chromatin-remodeling
complexes locally reposition the DNA
wrapped around nucleosomes. (A) The
complexes use energy derived from ATP
hydrolysis to loosen the nucleosomal DNA
and push it along the histone octamer,
thereby exposing the DNA to other DNAbinding proteins. The blue stripes have
been added to show how the nucleosome
moves along the DNA. Many cycles of
ATP hydrolysis are required to produce
such a shift. (B) In the case shown, the
repositioning of nucleosomes decondenses
the chromatin in a particular chromosomal
region; in other cases, it condenses the
chromatin.
(A)
ATP-dependent
chromatin-remodeling
complex
ADP
ATP
189
CATALYSIS OF
NUCLEOSOME SLIDING
remodeling
complex
(B)
ADP
ATP
condensed chromatin
decondensed chromatin
REPEATED ROUNDS OF
NUCLEOSOME SLIDING
another indicates that the genes in that stretch of chromatin should be
expressed; still others indicate that the nearby genes should be silenced
(Figure 5–27C).
Like the chromatin-remodeling complexes, the enzymes that modify
histone tails are tightly regulated. They are brought to particular chroECB4 e5.27/5.26
matin regions mainly by interactions with proteins that bind to specific
(A)
(C)
H4 tail
H2B tail
H3 histone modification state
H3 tail
H2A tail
H2A tail
heterochromatin
formation,
gene silencing
M
H4 tail
K
9
H2B tail
H3 tail
(B)
Ac
M
Ac
M
Ac
M
Ac
M
M P
M M
P
Ac
M
R K
KS
K
RK
K
RK S
K
2
9 10
14
1718
23
26 2728
36
4
meaning
M
histone
H3
M
Ac
K
K
4
9
gene expression
P
Ac
S
K
10
14
gene expression
Figure 5–27 The pattern of modification of histone tails can dictate how a stretch of chromatin is treated by the cell.
(A) Schematic drawing showing the positions of the histone tails that extend from each nucleosome. (B) Each histone can be modified
by the covalent attachment of a number of different chemical groups, mainly to the tails. Histone H3, for example, can receive an acetyl
group (Ac), a methyl group (M), or a phosphate group (P). The numbers denote the positions of the modified amino acids in the protein
chain, with each amino acid designated by its one-letter code. Note that some positions, such as lysines (K) 9, 14, 23, and 27, can be
modified in more than one way. Moreover, lysines can be modified with either one, two, or three methyl groups (not shown). Note that
histone H3 contains 135 amino acids, most of which are in its
globular
portion (green), and that most modifications are on its N-terminal
ECB4
e5.28/5.27
tail (orange). (C) Different combinations of histone tail modifications can confer a specific meaning on the stretch of chromatin on which
they occur, as indicated. Only a few of these “meanings” are known.
190
Chapter 5
DNA and Chromosomes
sequences in DNA (we discuss these proteins in Chapter 8). The histonemodifying enzymes work in concert with the chromatin-remodeling
complexes to condense or decondense stretches of chromatin, allowing
local chromatin structure to change rapidly according to the needs of the
cell.
Interphase Chromosomes Contain Both Condensed and
More Extended Forms of Chromatin
The localized alteration of chromatin packing by remodeling complexes
and histone modification has important effects on the large-scale structure of interphase chromosomes. Interphase chromatin is not uniformly
packed. Instead, regions of the chromosome that contain genes that are
being expressed are generally more extended, while those that contain
silent genes are more condensed. Thus, the detailed structure of an interphase chromosome can differ from one cell type to the next, helping to
determine which genes are expressed. Most cell types express about 20
to 30 % of the genes they contain.
The most highly condensed form of interphase chromatin is called heterochromatin (from the Greek heteros, “different,” plus chromatin). It was
first observed in the light microscope in the 1930s as discrete, strongly
staining regions within the mass of chromatin. Heterochromatin typically
makes up about 10% of an interphase chromosome, and in mammalian
chromosomes, it is concentrated around the centromere region and in
the telomeres at the ends of the chromosomes (see Figure 5–15).
The rest of the interphase chromatin is called euchromatin (from the
Greek eu, “true” or “normal,” plus chromatin). Although we use the term
euchromatin to refer to chromatin that exists in a more decondensed
state than heterochromatin, it is now clear that both euchromatin and
heterochromatin are composed of mixtures of different chromatin structures (Figure 5–28).
Each type of chromatin structure is established and maintained by
different sets of histone tail modifications that attract distinct sets of nonhistone proteins. The modifications that direct the formation of the most
common type of heterochromatin, for example, include the methylation
of lysine 9 in histone H3 (see Figure 5–27). Once it has been established,
heterochromatin can spread because these histone tail modifications
attract a set of heterochromatin-specific proteins, including histone-modifying enzymes, which then create the same histone tail modifications on
adjacent nucleosomes. These modifications in turn recruit more of the
heterochromatin-specific proteins, causing a wave of condensed chromatin to propagate along the chromosome. This heterochromatin will
continue to spread until it encounters a barrier DNA sequence that stops
the propagation (Figure 5–29). In this manner, extended regions of heterochromatin can be established along the DNA.
heterochromatin
telomere
euchromatin
heterochromatin
centromere
euchromatin
heterochromatin
euchromatin
heterochromatin
telomere
Figure 5–28 The structure of chromatin varies along a single interphase chromosome. As schematically indicated by different
colors (and the path of the DNA molecule represented by the central black line), heterochromatin and euchromatin each represent
a set of different chromatin structures with different degrees of condensation. Overall, heterochromatin is more condensed than
euchromatin.
The Regulation of Chromosome Structure
heterochromatin-specific,
histone tail modifications
barrier DNA
sequence
heterochromatin
euchromatin
HISTONE MODIFICATIONS ATTRACT
HETEROCHROMATIN-SPECIFIC PROTEINS,
INCLUDING HISTONE-MODIFYING ENZYMES
Figure 5–29 Heterochromatin-specific
modifications allow heterochromatin to
form and to spread. These modifications
attract heterochromatin-specific proteins
that reproduce the same modifications
on neighboring histones. In this manner,
heterochromatin can spread until it
encounters a barrier DNA sequence that
blocks its propagation into regions of
euchromatin.
HETEROCHROMATIN-SPECIFIC PROTEINS
MODIFY NEARBY HISTONES
HETEROCHROMATIN SPREADS
UNTIL IT ENCOUNTERS A
BARRIER DNA SEQUENCE
ECB4 n5.100/5.29
Most DNA that is permanently folded into heterochromatin in the cell
does not contain genes. Because heterochromatin is so compact, genes
that accidentally become packaged into heterochromatin usually fail to
be expressed. Such inappropriate packaging of genes in heterochromatin
can cause disease: in humans, the gene that encodes β-globin—which
forms part of the oxygen-carrying hemoglobin molecule—is situated next
to a region of heterochromatin. If, because of an inherited DNA deletion,
that heterochromatin spreads, the β-globin gene is poorly expressed and
the person develops a severe form of anemia.
Perhaps the most striking example of the use of heterochromatin to keep
genes shut down, or silenced, is found in the interphase X chromosomes
of female mammals. In mammals, female cells contain two X chromosomes, whereas male cells contain one X and one Y. Because a double
dose of X-chromosome products would be lethal, female mammals have
evolved a mechanism for permanently inactivating one of the two X
chromosomes in each cell. At random, one or other of the two X chromosomes in each cell becomes highly condensed into heterochromatin
early in embryonic development. Thereafter, the condensed and inactive
state of that X chromosome is inherited in all of the many descendants of
those cells (Figure 5–30).
When a cell divides, it generally passes on its histone modifications, chromatin structure, and gene expression patterns to the two daughter cells.
Such “cell memory” is critical for the establishment and maintenance
of different cell types during the development of a complex multicellular organism. We discuss the mechanisms involved in cell memory in
Chapter 8, where we consider the control of gene expression.
Question 5–4
Mutations in a particular gene on
the X chromosome result in color
blindness in men. By contrast, most
women carrying the mutation have
proper color vision but see colored
objects with reduced resolution, as
though functional cone cells (the
photoreceptor cells responsible for
color vision) are spaced farther apart
than normal in the retina. Can you
give a plausible explanation for this
observation? If a woman is colorblind, what could you say about her
father? About her mother? Explain
your answers.
191
192
Chapter 5
DNA and Chromosomes
Figure 5–30 One of the two X chromosomes
is inactivated in the cells of mammalian
females by heterochromatin formation. Each
female cell contains two X chromosomes, one
from the mother (Xm) and the other from the
father (Xp). At an early stage in embryonic
development, one of these two chromosomes
becomes condensed into heterochromatin
in each cell, apparently at random. At each
cell division, the same X chromosome
becomes condensed (and inactivated) in all
the descendants of that original cell. Thus,
all mammalian females end up as mixtures
(mosaics) of cells bearing maternal or paternal
inactivated X chromosomes. In most of their
tissues and organs, about half the cells will be of
one type, and the other half will be of the other.
cell in early embryo
Xp
Xm
INACTIVATION OF A RANDOMLY
SELECTED X CHROMOSOME
Xp
Xm
Xp
Xm
DIRECT INHERITANCE OF THE PATTERN OF X-CHROMOSOME INACTIVATION
only Xm active in this clone
only Xp active in this clone
Essential Concepts
•
Life depends on the stable
storage and inheritance of genetic
ECB4 e5.30/5.30
information.
•
Genetic information is carried by very long DNA molecules and is
encoded in the linear sequence of four nucleotides: A, T, G, and C.
•
Each molecule of DNA is a double helix composed of a pair of
antiparallel, complementary DNA strands, which are held together
by hydrogen bonds between G-C and A-T base pairs.
•
The genetic material of a eukaryotic cell is contained in a set of chromosomes, each formed from a single, enormously long DNA molecule
that contains many genes.
•
When a gene is expressed, part of its nucleotide sequence is transcribed into RNA molecules, many of which are translated into
protein.
•
The DNA that forms each eukaryotic chromosome contains, in addition to genes, many replication origins, one centromere, and two
telomeres. These special DNA sequences ensure that, before cell
division, each chromosome can be duplicated efficiently, and that
the resulting daughter chromosomes are parceled out equally to the
two daughter cells.
•
In eukaryotic chromosomes, the DNA is tightly folded by binding to
a set of histone and nonhistone proteins. This complex of DNA and
protein is called chromatin.
•
Histones pack the DNA into a repeating array of DNA–protein particles called nucleosomes, which further fold up into even more
compact chromatin structures.
193
Chapter 5 End-of-Chapter Questions
•
A cell can regulate its chromatin structure—temporarily decondensing or condensing particular regions of its chromosomes—using
chromatin-remodeling complexes and enzymes that covalently modify histone tails in various ways.
•
The loosening of chromatin to a more decondensed state allows proteins involved in gene expression, DNA replication, and DNA repair to
gain access to the necessary DNA sequences.
•
Some forms of chromatin have a pattern of histone tail modification
that causes the DNA to become so highly condensed that its genes
cannot be expressed to produce RNA; such condensation occurs on
all chromosomes during mitosis and in the heterochromatin of interphase chromosomes.
Key terms
base pair
cell cycle
centromere
chromatin
chromatin-remodeling complex
chromosome
complementary
deoxyribonucleic acid (DNA)
double helix
euchromatin
gene
gene expression
genetic code
genome
heterochromatin
histone
karyotype
nucleolus
nucleolus
replication origin
telomere gene
Questions
Question 5–5
A. The nucleotide sequence of one DNA strand of a DNA
double helix is
3′
5′
3′
5′
5’-GGATTTTTGTCCACAATCA-3’.
What is the sequence of the complementary strand?
H
B.In the DNA of certain bacterial cells, 13% of the
nucleotides are adenine. What are the percentages of the
other nucleotides?
C.How many possible nucleotide sequences are there for a
stretch of DNA that is N nucleotides long, if it is (a) singlestranded or (b) double-stranded?
D. Suppose you had a method of cutting DNA at specific
sequences of nucleotides. How many nucleotides long
(on average) would such a sequence have to be in order
to make just one cut in a bacterial genome of 3 × 106
nucleotide pairs? How would the answer differ for the
genome of an animal cell that contains 3 × 109 nucleotide
pairs?
N
O
C
C
C
N
C
N
adenine
C
N
C
N
cytosine
N
N
H
H
H
H
H
H
H
C
N
C
N
H
C
H
H
N
H
C
N
C
3′
C
N
H
N
adenine
Question 5–6
An A-T base pair is stabilized by only two hydrogen bonds.
Hydrogen-bonding schemes of very similar strengths can
also be drawn between other base combinations that
normally do not occur in DNA molecules, such as the A-C
and the A-G pairs shown in Figure Q5–6.
C
C
N
N
guanine
C
O
H
N
H
C
C
C
N
N
C
H
5′
Figure Q5–6
5′
3′
194
Chapter 5
DNA and Chromosomes
What would happen if these pairs formed during DNA
replication and the inappropriate bases were incorporated?
Discuss why this does not often happen. (Hint: see
Figure 5–6.)
Question 5–7
A. A macromolecule isolated from an extraterrestrial source
superficially resembles DNA, but closer analysis reveals that
the bases have quite different structures (Figure Q5–7).
Bases V, W, X, and Y have replaced bases A, T, G, and C.
Look at these structures closely. Could these DNA-like
molecules have been derived from a living organism that
uses principles of genetic inheritance similar to those used
by organisms on Earth?
Figure 5–6B) at an interval of 0.34 nm. If the DNA were
enlarged so that its diameter equaled that of an electrical
extension cord (5 mm), how long would the extension cord
be from one end to the other (assuming that it is completely
stretched out)? How close would the bases be to each
other? How long would a gene of 1000 nucleotide pairs be?
Question 5–10
A compact disc (CD) stores about 4.8 × 109 bits of
information in a 96 cm2 area. This information is stored as a
binary code—that is, every bit is either a 0 or a 1.
A.How many bits would it take to specify each nucleotide
pair in a DNA sequence?
B.How many CDs would it take to store the information
contained in the human genome?
H
N
H
N
C
H
O
C
C
N
H
C
C
V
C
C
O
O
H
H
H
N
N
N
X
C
C
C
N
Question 5–11
H
H
N
C
H
N
C
N
H
Y
C
N
N
W
C
N
H
H
N
O
C
N
Which of the following statements are correct? Explain your
answers.
C
H
A. Each eukaryotic chromosome must contain the following
DNA sequence elements: multiple origins of replication, two
telomeres, and one centromere.
B. Nucleosome core particles are 30 nm in diameter.
Question 5–12
C
N
C
H
Define the following terms and their relationships to one
another:
A.Interphase chromosome
H
B. Mitotic chromosome
C. Chromatin
D. Heterochromatin
Figure Q5–7
B. Simply judgedECB4
by their
potential for hydrogen-bonding,
EQ5.08/Q5.07
could any of these extraterrestrial bases replace terrestrial
A, T, G, or C in terrestrial DNA? Explain your answer.
Question 5–8
The two strands of a DNA double helix can be separated
by heating. If you raised the temperature of a solution
containing the following three DNA molecules, in what
order do you suppose they would “melt”? Explain your
answer.
E. Histones
F. Nucleosome
Question 5–13
Carefully consider the result shown in Figure Q5–13.
Each of the two colonies shown on the left is a clump of
approximately 100,000 yeast cells that has grown up from
a single cell, which is now somewhere in the middle of the
colony. The two yeast colonies are genetically different, as
shown by the chromosomal maps on the right.
A. 5’-GCGGGCCAGCCCGAGTGGGTAGCCCAGG-3’
telomere
3’-CGCCCGGTCGGGCTCACCCATCGGGTCC-5’
B. 5’-ATTATAAAATATTTAGATACTATATTTACAA-3’
3’-TAATATTTTATAAATCTATGATATAAATGTT-5’
Ade2 gene at normal location
on chromosome
white colony of
yeast cells
C. 5’-AGAGCTAGATCGAT-3’
3’-TCTCGATCTAGCTA-5’
Ade2 gene moved near a telomere
Question 5–9
The total length of DNA in the human genome is about
1 m, and the diameter of the double helix is about 2 nm.
Nucleotides in a DNA double helix are stacked (see
red colony of
yeast cells
with white sectors
Figure Q5–13
telomere
Chapter 5 End-of-Chapter Questions
The yeast Ade2 gene encodes one of the enzymes required
for adenine biosynthesis, and the absence of the Ade2 gene
product leads to the accumulation of a red pigment. At its
normal chromosome location, Ade2 is expressed in all cells.
When it is positioned near the telomere, which is highly
condensed, Ade2 is no longer expressed. How do you think
the white sectors arise? What can you conclude about the
propagation of the transcriptional state of the Ade2 gene
from mother to daughter cells?
195
Question 5–15
DNA forms a right-handed helix. Pick out the right-handed
helix from those shown in Figure Q5–15.
(A)
(B)
(C)
Question 5–14
The two electron micrographs in Figure Q5–14 show nuclei
of two different cell types. Can you tell from these pictures
which of the two cells is transcribing more of its genes?
Explain how you arrived at your answer. (Micrographs
courtesy of Don W. Fawcett.)
Figure Q5–15
Question 5–16
A single nucleosome core particle is 11 nm in diameter and
contains 147 bp of DNA (the DNA double helix measures
ECB4 EQ5.16/Q5.15
0.34 nm/bp). What packing ratio (ratio of DNA length to
nucleosome diameter) has been achieved by wrapping DNA
around the histone octamer? Assuming that there are an
additional 54 bp of extended DNA in the linker between
nucleosomes, how condensed is “beads-on-a-string” DNA
relative to fully extended DNA? What fraction of the
10,000-fold condensation that occurs at mitosis does this
first level of packing represent?
(A)
(B)
Figure Q5–14
ECB4 EQ5.15/Q5.14
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chapter six
6
DNA Replication, Repair, and
Recombination
The ability of a cell to survive and proliferate in a chaotic environment
depends on the accurate duplication of the vast quantity of genetic information carried in its DNA. This duplication process, called DNA replication,
must occur before a cell can divide to produce two genetically identical
daughter cells. Maintaining order in a cell also requires the continual
surveillance and repair of its genetic information, as DNA is subjected to
unavoidable damage by chemicals and radiation in the environment and
by reactive molecules that are generated inside the cell. In this chapter,
we describe the protein machines that replicate and repair the cell’s DNA.
These machines catalyze some of the most rapid and accurate processes that take place within cells, and the strategies they have evolved to
achieve this feat are marvels of elegance and efficiency.
Despite these systems for protecting a cell’s DNA from copying errors
and accidental damage, permanent changes—or mutations—sometimes
do occur. Although most mutations do not affect the organism in any
noticeable way, some have profound consequences. Occasionally, these
changes can benefit the organism: for example, mutations can make
bacteria resistant to antibiotics that are used to kill them. What is more,
changes in DNA sequence can produce small variations that underlie the
differences between individuals of the same species (Figure 6–1); when
allowed to accumulate over millions of years, such changes provide the
variety in genetic material that makes one species distinct from another,
as we discuss in Chapter 9.
But, mutations are much more likely to be detrimental than beneficial: in
humans, they are responsible for thousands of genetic diseases, including
cancer. The survival of a cell or organism, therefore, depends on keeping
dna replication
dna repair
198
Chapter 6
DNA Replication, Repair, and Recombination
Figure 6–1 Genetic information is passed from one generation to
the next. Differences in DNA can produce the variations that underlie
the differences between individuals of the same species—or, over
time, the differences between one species and another. In this family
photo, the children resemble one another and their parents more
closely than they resemble other people because they inherit their
genes from their parents. The cat shares many features with humans,
but during the millions of years of evolution that have separated
humans and cats, both have accumulated many changes in DNA that
now make the two species different. The chicken is an even more
distant relative.
changes in its DNA to a minimum. Without the protein machines that are
continually monitoring and repairing damage to DNA, it is questionable
whether life could exist at all.
DNA Replication
At each cell division, a cell must copy its genome with extraordinary
accuracy. In this section, we explore how the cell achieves this feat, while
duplicating its DNA at rates as high as 1000 nucleotides per second.
Base-Pairing Enables DNA Replication
In the preceding chapter, we saw that each strand of a DNA double helix
contains a sequence of nucleotides that is exactly complementary to
the nucleotide sequence of its partner strand. Each strand can therefore
serve as a template, or mold, for the synthesis of a new complementary
strand. In other words, if we designate the two DNA strands as S and Sʹ,
strand S can serve as a template for making a new strand Sʹ, while strand
Sʹ can serve as a template for making a new strand S (Figure 6–2). Thus,
the genetic information in DNA can be accurately copied by the beautifully simple process in which strand S separates from strand Sʹ, and each
separated strand then serves as a template for the production of a new
complementary partner strand that is identical to its former partner.
ECB4 e6.01/6.01
The ability of each strand of a DNA molecule to act as a template for
producing a complementary strand enables a cell to copy, or replicate,
its genes before passing them on to its descendants. But the task is aweinspiring, as it can involve copying billions of nucleotide pairs every time
a cell divides. The copying must be carried out with incredible speed and
accuracy: in about 8 hours, a dividing animal cell will copy the equivalent
of 1000 books like this one and, on average, get no more than a few letters wrong. This impressive feat is performed by a cluster of proteins that
together form a replication machine.
template S strand
5′
Figure 6–2 DNA acts as a template
for its own duplication. Because the
nucleotide A will successfully pair only
with T, and G with C, each strand of a
DNA double helix—labeled here as
the S strand and its complementary
Sʹ strand—can serve as a template to
specify the sequence of nucleotides in its
complementary strand. In this way, both
strands of a DNA double helix can be
copied precisely.
S strand
5′
C
G
3′
A
T
T
T
A
A
G
C
C
C
G
G
A
T
S′ strand
G
T
C
A
3′
5′
3′
C
A
T
T
G
C
C
A
G
T
G
T
A
A
C
G
G
T
C
A
3′
5′
new S′ strand
new S strand
5′
parent DNA double helix
3′
C
A
T
T
G
C
C
A
G
T
G
T
A
A
C
G
G
T
C
A
template S′ strand
3′
5′
DNA Replication
199
Figure 6–3 In each round of DNA replication, each of the two
strands of DNA is used as a template for the formation of a new,
complementary strand. DNA replication is “semiconservative”
because each daughter DNA double helix is composed of one
conserved strand and one newly synthesized strand.
REPLICATION
DNA replication produces two complete double helices from the original
DNA molecule, with each new DNA helix being identical (except for rare
copying errors) in nucleotide sequence to the original DNA double helix
(see Figure 6–2). Because each parental strand serves as the template for
one new strand, each of the daughter DNA double helices ends up with
one of the original (old) strands plus one strand that is completely new;
this style of replication is said to be semiconservative (Figure 6–3). In How
We Know, pp. 200–202, we discuss the experiments that first demonstrated that DNA is replicated in this way.
REPLICATION
DNA Synthesis Begins at Replication Origins
REPLICATION
The DNA double helix is normally very stable: the two DNA strands are
locked together firmly by the large numbers of hydrogen bonds between
the bases on both strands (see Figure 5–2). As a result, only temperatures
approaching those of boiling water provide enough thermal energy to
separate the two strands. To be used as a template, however, the double
helix must first be opened up and the two strands separated to expose
unpaired bases. How does this occur at the temperatures found in living
cells?
The process of DNA synthesis is begun by initiator proteins that bind to
specific DNA sequences called replication origins. Here, the initiator
proteins pry the two DNA strands apart, breaking the hydrogen bonds
between the bases (Figure 6–4). Although the hydrogen bonds collectively make the DNA helix very stable, individually each hydrogen bond
is weak (as discussed in Chapter 2). Separating a short length of DNA a
few base pairs at a time therefore does not require a large energy input,
and the initiator proteins can readily unzip the double helix at normal
temperatures.
ECB4 e6.04/6.03
In simple cells such as bacteria or yeast, replication origins span approximately 100 nucleotide pairs. They are composed of DNA sequences that
attract the initiator proteins and are especially easy to open. We saw in
Chapter 5 that an A-T base pair is held together by fewer hydrogen bonds
than is a G-C base pair. Therefore, DNA rich in A-T base pairs is relatively
easy to pull apart, and A-T-rich stretches of DNA are typically found at
replication origins.
A bacterial genome, which is typically contained in a circular DNA molecule of several million nucleotide pairs, has a single replication origin.
The human genome, which is very much larger, has approximately 10,000
such origins—an average of 220 origins per chromosome. Beginning
DNA replication at many places at once greatly shortens the time a cell
needs to copy its entire genome.
Once an initiator protein binds to DNA at a replication origin and locally
opens up the double helix, it attracts a group of proteins that carry out
DNA replication. These proteins form a replication machine, in which
each protein carries out a specific function.
Two Replication Forks Form at Each Replication Origin
DNA molecules in the process of being replicated contain Y-shaped
junctions called replication forks. Two replication forks are formed at
5′
3′
doublereplication origin helical
DNA
3′
5′
double helix opened
with the aid of
initiator proteins
5′
3′
3′
5′
single-stranded DNA templates
ready for DNA synthesis
Figure 6–4 A DNA double helix is opened
at replication origins. DNA sequences at
replication origins are recognized by initiator
proteins (not shown), which locally pry apart
the two strands of the double helix. The
exposed single strands can then serve as
templates for copying the DNA.
ECB4 e6.05/6.04
200
How we Know
THE NATURE OF REPLICATION
In 1953, James Watson and Francis Crick published
their famous two-page paper describing a model for the
structure of DNA (see Figure 5–2). In it, they proposed
that complementary bases—adenine and thymine, guanine and cytosine—pair with one another along the
center of the double helix, holding together the two
strands of DNA. At the very end of this succinct scientific blockbuster, they comment, almost as an aside, “It
has not escaped our notice that the specific pairing we
have postulated immediately suggests a possible copying mechanism for the genetic material.”
Indeed, one month after the classic paper appeared in
print in the journal Nature, Watson and Crick published
a second article, suggesting how DNA might be duplicated. In this paper, they proposed that the two strands
of the double helix unwind, and that each strand serves
as a template for the synthesis of a complementary
daughter strand. In their model, dubbed semiconservative replication, each new DNA molecule consists of one
strand derived from the original parent molecule and
one newly synthesized strand (Figure 6–5A).
We now know that Watson and Crick’s model for DNA
replication was correct—but it was not universally
accepted at first. Respected physicist-turned-geneticist
Max Delbrück, for one, got hung up on what he termed
“the untwiddling problem;” that is: how could the two
strands of a double helix, twisted around each other
so many times all along their great length, possibly be
unwound without making a big tangled mess? Watson
and Crick’s conception of the DNA helix opening up like
a zipper seemed, to Delbrück, physically unlikely and
simply “too inelegant to be efficient.”
Instead, Delbrück proposed that DNA replication proceeds through a series of breaks and reunions, in which
the DNA backbone is broken and the strands are copied in short segments—perhaps only 10 nucleotides at
a time—before being rejoined. In this model, which was
later dubbed dispersive, the resulting copies would be
patchwork collections of old and new DNA, each strand
containing a mixture of both (Figure 6–5B). No unwinding was necessary.
Yet a third camp promoted the idea that DNA replication might be conservative: that the parent helix would
somehow remain entirely intact after copying, and the
daughter molecule would contain two entirely new DNA
strands (Figure 6–5C). To determine which of these
models was correct, an experiment was needed—one
that would reveal the composition of the newly synthesized DNA strands. That’s where Matt Meselson and
Frank Stahl came in.
As a graduate student working with Linus Pauling,
Meselson was toying with a method for telling the difference between old and new proteins. After chatting with
Delbrück about Watson and Crick’s replication model, it
after one
generation
(A)
SEMICONSERVATIVE
(B)
DISPERSIVE
(C)
CONSERVATIVE
Figure 6–5 Three models for DNA replication make different predictions. (A) In the semiconservative model, each parent strand
serves as a template for the synthesis of a new daughter strand. The first round of replication would produce two hybrid molecules,
each containing one strand from the original parent in addition to one newly synthesized strand. A subsequent round of replication
would yield two hybrid molecules and two molecules that contain none of the original parent DNA (see Figure 6–3). (B) In the dispersive
model, each generation of daughter DNA will contain a mixture of DNA from the parent strands and the newly synthesized DNA.
(C) In the conservative model, the parent molecule remains intact after being copied. In this case, the first round of replication would
ECB4
e6.06/6.05
yield the original parent double helix and an entirely new
double
helix. For each model, parent DNA molecules are shown in orange;
newly replicated DNA is red. Note that only a very small segment of DNA is shown for each model.
DNA Replication
occurred to Meselson that the approach he’d envisaged
for exploring protein synthesis might also work for studying DNA. In the summer of 1954, Meselson met Stahl,
who was then a graduate student in Rochester, NY, and
they agreed to collaborate. It took a few years to get
everything working, but the two eventually performed
what has come to be known as “the most beautiful
experiment in biology.”
Their approach, in retrospect, was stunningly straightforward. They started by growing two batches of E. coli
bacteria, one in a medium containing a heavy isotope
of nitrogen, 15N, the other in a medium containing the
normal, lighter 14N. The nitrogen in the nutrient medium
gets incorporated into the nucleotide bases and, from
there, makes its way into the DNA of the organism.
After growing bacterial cultures for many generations in
either the 15N- or 14N-containing medium, the researchers had two flasks of bacteria, one whose DNA was
heavy, the other whose DNA was light. Meselson and
Stahl then broke open the bacterial cells and loaded the
DNA into tubes containing a high concentration of the
salt cesium chloride. When these tubes are centrifuged
at high speed, the cesium chloride forms a density gradient, and the DNA molecules float or sink within the
solution until they reach the point at which their density
equals that of the surrounding salt solution (see Panel
4–3, pp. 164–165). Using this method, called equilibrium
ISOLATE 15N-DNA
AND LOAD INTO
CENTRIFUGE
TUBE
bacteria grown in
medium
15N-containing
heavy 15N-DNA forms a
high-density band, closer
to the bottom of the tube
201
density centrifugation, Meselson and Stahl found that
they could distinguish between heavy (15N-containing)
DNA and light (14N-containing) DNA by observing the
positions of the DNA within the cesium chloride gradient. Because the heavy DNA was denser than the light
DNA, it collected at a position nearer to the bottom of
the centrifuge tube (Figure 6–6).
Once they had established this method for differentiating between light and heavy DNA, Meselson and Stahl
set out to test the various hypotheses proposed for DNA
replication. To do this, they took a flask of bacteria that
had been grown in heavy nitrogen and transferred the
bacteria into a medium containing the light isotope. At
the start of the experiment, all the DNA would be heavy.
But, as the bacteria divided, the newly synthesized DNA
would be light. They could then monitor the accumulation of light DNA and see which model, if any, best fit the
data. After one generation of growth, the researchers
found that the parental, heavy DNA molecules—those
made of two strands containing 15N—had disappeared
and were replaced by a new species of DNA that banded
at a density halfway between those of 15N-DNA and 14NDNA (Figure 6–7). These newly synthesized daughter
helices, Meselson and Stahl reasoned, must be hybrids—
containing both heavy and light isotopes.
Right away, this observation ruled out the conservative model of DNA replication, which predicted that
ISOLATE 14N-DNA
AND LOAD INTO
CENTRIFUGE
TUBE
CENTRIFUGE AT HIGH SPEED
FOR 48h TO FORM CESIUM
CHLORIDE DENSITY GRADIENT
light 14N-DNA forms a
low-density band, closer
to the top of the tube
bacteria grown in
medium
14N-containing
Figure 6–6 Centrifugation in a
cesium chloride gradient allows
the separation of heavy and light
DNA. Bacteria are grown for several
generations in a medium containing
either 15N (the heavy isotope) or 14N
(the light isotope) to label their DNA.
The cells are then broken open, and the
DNA is loaded into an ultracentrifuge
tube containing a cesium chloride salt
solution. These tubes are centrifuged
at high speed for two days to allow
the DNA to collect in a region where
its density matches that of the salt
surrounding it. The heavy and light
DNA molecules collect in different
positions in the tube.
202
Chapter 6
DNA Replication, Repair, and Recombination
CONDITION
RESULT
INTERPRETATION
centrifugal force
light DNA
molecules
(A) bacteria grown in
light medium
centrifugal force
heavy DNA
molecules
(B) bacteria grown in
heavy medium
TRANSFER TO
LIGHT MEDIUM
OR
centrifugal force
(C) bacteria grown an
additional 20 min in
light medium
DNA molecules of intermediate weight
Figure 6–7 The first part of the Meselson–Stahl experiment ruled out the
conservative model of DNA replication. (A) Bacteria grown in light medium
(containing 14N) yield DNA that forms a band high up in the centrifuge tube, whereas
bacteria grown in 15N-containing heavy medium (B) produce DNA that migrates
further down the tube. When bacteria grown in a heavy medium are transferred
to a light medium and allowed to continue dividing, they produce a band whose
position falls somewhere between that of the parent bands (C). These results rule
ECB4 e6.08/6.07
out the conservative model of replication but do not distinguish between the
semiconservative and dispersive models, both of which predict the formation of hybrid
daughter DNA molecules.
The fact that the results came out looking so clean—with discrete bands forming
at the expected positions for newly replicated hybrid DNA molecules—was a happy
accident of the experimental protocol. The researchers used a hypodermic syringe to
load their DNA samples into the ultracentrifuge tubes (see Figure 6–6). In the process,
they unwittingly sheared the large bacterial chromosome into smaller fragments.
Had the chromosomes remained whole, the researchers might have isolated DNA
molecules that were only partially replicated, because many cells would have been
caught in the middle of copying their DNA. Molecules in such an intermediate stage
of replication would not have separated into such discrete bands. But because the
researchers were instead working with smaller pieces of DNA, the likelihood that any
given fragment had been fully replicated—and contained a complete parent and
daughter strand—was high, thus yielding nice, clean results.
the parental DNA would remain
entirely heavy, while the daughter
DNA would be entirely light (see
Figure 6–5C). The data matched with
the semiconservative model, which
predicted the formation of hybrid
molecules containing one strand of
heavy DNA and one strand of light
(see Figure 6–5A). The results, however, were also consistent with the
dispersive model, in which hybrid
DNA strands would contain a mixture of heavy and light DNA (see
Figure 6–5B).
To distinguish between the two
models, Meselson and Stahl turned
up the heat. When DNA is subjected to high temperature, the
hydrogen bonds holding the two
strands together break and the
helix comes apart, leaving a collection of single-stranded DNAs. When
the researchers heated their hybrid
molecules before centrifuging, they
discovered that one strand of the
DNA was heavy, whereas the other
was light. This observation supported only the semiconservative
model; if the dispersive model were
correct, the resulting strands, each
containing a mottled assembly of
heavy and light DNA, would have all
banded together at an intermediate
density.
According to historian Frederic
Lawrence Holmes, the experiment
was so elegant and the results
so clean that Stahl—when being
interviewed for a position at Yale
University—was unable to fill the 50
minutes allotted for his talk. “I was
finished in 25 minutes,” said Stahl,
“because that is all it takes to tell that
experiment. It’s so totally simple and
contained.” Stahl did not get the job
at Yale, but the experiment convinced
biologists that Watson and Crick had
been correct. In fact, the results were
accepted so widely and rapidly that
the experiment was described in a
textbook before Meselson and Stahl
had even published the data.
DNA Replication
each replication origin (Figure 6–8). At each fork, a replication machine
moves along the DNA, opening up the two strands of the double helix
and using each strand as a template to make a new daughter strand. The
two forks move away from the origin in opposite directions, unzipping
the DNA double helix and replicating the DNA as they go (Figure 6–9).
DNA replication in bacterial and eukaryotic chromosomes is therefore
termed bidirectional. The forks move very rapidly—at about 1000 nucleotide pairs per second in bacteria and 100 nucleotide pairs per second
in humans. The slower rate of fork movement in humans (indeed, in all
eukaryotes) may be due to the difficulties in replicating DNA through the
more complex chromatin structure of eukaryotic chromosomes.
replication forks
replication
origin
template DNA
newly synthesized DNA
Figure 6–8 DNA synthesis occurs at
Y-shaped junctions called replication
forks. Two replication forks are formed at
ECB4 n6.100/6.08
each replication
origin.
DNA Polymerase Synthesizes DNA Using a Parental Strand
as Template
The movement of a replication fork is driven by the action of the replication machine, at the heart of which is an enzyme called DNA polymerase.
This enzyme catalyzes the addition of nucleotides to the 3ʹ end of a growing DNA strand, using one of the original, parental DNA strands as a
template. Base pairing between an incoming nucleotide and the template
strand determines which of the four nucleotides (A, G, T, or C) will be
selected. The final product is a new strand of DNA that is complementary
in nucleotide sequence to the template (Figure 6–10).
The polymerization reaction involves the formation of a phosphodiester
bond between the 3ʹ end of the growing DNA chain and the 5ʹ-phosphate
group of the incoming nucleotide, which enters the reaction as a deoxyribonucleoside triphosphate. The energy for polymerization is provided
origins of replication
1
direction of
fork movement
2
replication forks
Question 6–1
3
(A)
(B)
0.1 µm
Figure 6–9 The two replication forks move away in opposite directions at
each replication origin. (A) These drawings represent the same portion of a DNA
molecule as it might appear at different times during replication. The orange
lines represent the two parental DNA strands; the red lines represent the newly
synthesized DNA strands. (B) An electron micrograph showing DNA replicating in
an early fly embryo. The particles visible along the DNA are nucleosomes, structures
made of DNA and the protein complexes around which the DNA is wrapped
(discussed in Chapter 5). The chromosome in this micrograph is the one that was
redrawn in sketch (2) above. (Electron micrograph courtesy of Victoria Foe.)
Look carefully at the micrograph and
drawing 2 in Figure 6–9.
A. Using the scale bar, estimate the
lengths of the DNA strands between
the replication forks. Numbering the
replication forks sequentially from
the left, how long will it take until
forks 4 and 5, and forks 7 and 8,
respectively, collide with each other?
(Recall that the distance between
the bases in DNA is 0.34 nm, and
eukaryotic replication forks move at
about 100 nucleotides per second.)
For this question, disregard the
nucleosomes seen in the micrograph
and assume that the DNA is fully
extended.
B. The fly genome is about
1.8 × 108 nucleotide pairs in size.
What fraction of the genome is
shown in the micrograph?
203
204
Chapter 6
DNA Replication, Repair, and Recombination
new strand
5′
A
C
3′
C
A
T
T
G
G
T
A
A
C
3′
by the incoming deoxyribonucleoside triphosphate itself: hydrolysis
of one of its high-energy phosphate bonds fuels the reaction that links
the nucleotide monomer to the chain, releasing pyrophosphate (Figure
6–11). Pyrophosphate is further hydrolyzed to inorganic phosphate (Pi),
which makes the polymerization reaction effectively irreversible (see
Figure 3–41).
T
C
G
G
G
T
5′
template strand
Figure ECB4
6–10 Ae6.02/6.10
new DNA strand is
synthesized in the 5ʹ–to–3ʹ direction.
At each step, the appropriate incoming
nucleotide is selected by forming base pairs
with the next nucleotide in the template
strand: A with T, T with A, C with G, and G
with C. Each is added to the 3ʹ end of the
growing new strand, as indicated.
incoming
nucleotide
5′
new
strand
3′
OH
P P P
3′
5′ P
P
P
P
3′
P
P
P
OH
P
DNA polymerase does not dissociate from the DNA each time it adds a
new nucleotide to the growing strand; rather, it stays associated with the
DNA and moves along the template strand stepwise for many cycles of
the polymerization reaction (Movie 6.1). We will see later that a special
protein keeps the polymerase attached to the DNA, as it repeatedly adds
new nucleotides to the growing strand.
The Replication Fork Is Asymmetrical
The 5ʹ-to-3ʹ direction of the DNA polymerization reaction poses a problem
at the replication fork. As illustrated in Figure 5–2, the sugar–phosphate
backbone of each strand of a DNA double helix has a unique chemical
direction, or polarity, determined by the way each sugar residue is linked
to the next, and the two strands in the double helix are antiparallel; that
is, they run in opposite directions. As a consequence, at each replication fork, one new DNA strand is being made on a template that runs
in one direction (3ʹ to 5ʹ), whereas the other new strand is being made
on a template that runs in the opposite direction (5ʹ to 3ʹ) (Figure 6–12).
The replication fork is therefore asymmetrical. Looking at Figure 6–9A,
however, it appears that both of the new DNA strands are growing in the
same direction; that is, the direction in which the replication fork is moving. That observation suggests that one strand is being synthesized in the
5ʹ-to-3ʹ direction and the other in the 3ʹ-to-5ʹ direction.
P
P
P
P
3′
P
P
P
P
P P
pyrophosphate
P
P 5′
P
3′
5′ P
OH
P
P
5′-to-3′
direction of
chain growth
P 5′
template
strand
(A)
(C)
5′
template
strand
3′
5′
new
strand
DNA
polymerase
3′
INCOMING
NUCLEOTIDE
PAIRS WITH A
BASE IN THE
TEMPLATE STRAND
DNA POLYMERASE
CATALYZES COVALENT
LINKAGE OF
NUCLEOTIDE INTO
GROWING NEW STRAND
P Pi
(B)
Figure 6–11 DNA polymerase adds a deoxyribonucleotide to the 3ʹ end of a growing DNA chain. (A) Nucleotides enter the
reaction as deoxyribonucleoside triphosphates. This incoming nucleotide forms a base pair with its partner in the template strand.
It is then linked to the free 3ʹ hydroxyl on the growing DNA strand. The new DNA strand is therefore synthesized in the 5ʹ-to-3ʹ
direction. Breakage of a high-energy phosphate bond in the incoming nucleoside triphosphate—accompanied by the release of
pyrophosphate—provides the energy for the polymerization reaction. (B) The reaction is catalyzed by the enzyme DNA polymerase
(light green). The polymerase guides the incoming nucleotide to the template strand and positions it such that its 5ʹ terminal
phosphate will be able to react with the 3ʹ-hydroxyl group on the newly synthesized strand. The gray arrow indicates the direction of
polymerase movement. (C) Structure of DNA polymerase, as determined by X-ray crystallography, which shows the positioning of the
DNA double helix. The template strand is the longer of the two DNA strands (Movie 6.1).
ECB4 m5.04/6.11
DNA Replication
Does the cell have two types of DNA polymerase, one for each direction?
The answer is no: all DNA polymerases add new subunits only to the 3ʹ
end of a DNA strand (see Figure 6–11A). As a result, a new DNA chain
can be synthesized only in a 5ʹ-to-3ʹ direction. This can easily account
for the synthesis of one of the two strands of DNA at the replication fork,
but what happens on the other? This conundrum is solved by the use of
a “backstitching” maneuver. The DNA strand that appears to grow in the
incorrect 3ʹ-to-5ʹ direction is actually made discontinuously, in successive, separate, small pieces—with the DNA polymerase moving backward
with respect to the direction of replication-fork movement so that each
new DNA fragment can be polymerized in the 5ʹ-to-3ʹ direction.
The resulting small DNA pieces—called Okazaki fragments after the
biochemists who discovered them—are later joined together to form a
continuous new strand. The DNA strand that is made discontinuously in
this way is called the lagging strand, because the backstitching imparts
a slight delay to its synthesis; the other strand, which is synthesized continuously, is called the leading strand (Figure 6–13).
5′
3′
newly synthesized
strands
5′
3′
5′
3′
parental
DNA helix
205
3′
5′
direction of replicationfork movement
Figure 6–12 At a replication fork, the two
newly synthesized DNA strands are of
opposite polarities. This is because the two
template strands are oriented in opposite
directions.
ECB4 e6.11/6.12
Although they differ in subtle details, the replication forks of all cells,
prokaryotic and eukaryotic, have leading and lagging strands. This common feature arises from the fact that all DNA polymerases work only in
the 5ʹ-to-3ʹ direction—a restriction that provides cells with an important
advantage, as we discuss next.
DNA Polymerase Is Self-correcting
DNA polymerase is so accurate that it makes only about one error in
every 107 nucleotide pairs it copies. This error rate is much lower than
can be explained simply by the accuracy of complementary base-pairing.
Although A-T and C-G are by far the most stable base pairs, other, less
stable base pairs—for example, G-T and C-A—can also be formed. Such
incorrect base pairs are formed much less frequently than correct ones,
but, if allowed to remain, they would result in an accumulation of mutations. This disaster is avoided because DNA polymerase has two special
qualities that greatly increase the accuracy of DNA replication. First,
the enzyme carefully monitors the base-pairing between each incoming nucleotide and the template strand. Only when the match is correct
does DNA polymerase catalyze the nucleotide-addition reaction. Second,
Okazaki fragments
5′
3′
5′
3′
3′5′
3′ 5′
3′ 5′
3′
5′
direction of fork movement
leading-strand template
of left-hand fork
5′
3′
lagging-strand template
of left-hand fork
lagging-strand template
of right-hand fork
3′
most recently
synthesized DNA
5′
leading-strand template
of right-hand fork
Figure 6–13 At each replication fork, the
lagging DNA strand is synthesized in
pieces. Because both of the new strands
at a replication fork are synthesized in the
5ʹ-to-3ʹ direction, the lagging strand of
DNA must be made initially as a series of
short DNA strands, which are later joined
together. The upper diagram shows two
replication forks moving in opposite
directions; the lower diagram shows the
same forks a short time later. To replicate
the lagging strand, DNA polymerase uses
a backstitching mechanism: it synthesizes
short pieces of DNA (called Okazaki
fragments) in the 5ʹ-to-3ʹ direction and then
moves back along the template strand
(toward the fork) before synthesizing the
next fragment.
206
Chapter 6
DNA Replication, Repair, and Recombination
DNA polymerase
5′
3′
template
DNA strand
3′
5′
POLYMERASE ADDS AN
INCORRECT NUCLEOTIDE
3′
5′
3′
5′
MISPAIRED NUCLEOTIDE
REMOVED BY
PROOFREADING
5′
3′
3′
5′
CORRECTLY PAIRED 3′ END
ALLOWS ADDITION OF
NEXT NUCLEOTIDE
5′
Proofreading takes place at the same time as DNA synthesis. Before the
enzyme adds the next nucleotide to a growing DNA strand, it checks
whether the previously added nucleotide is correctly base-paired to the
template strand. If so, the polymerase adds the next nucleotide; if not,
the polymerase clips off the mispaired nucleotide and tries again (Figure
6–14). This proofreading is carried out by a nuclease that cleaves the
phosphodiester backbone. Polymerization and proofreading are tightly
coordinated, and the two reactions are carried out by different catalytic
domains in the same polymerase molecule (Figure 6–15).
This proofreading mechanism explains why DNA polymerases synthesize
DNA only in the 5ʹ-to-3ʹ direction, despite the need that this imposes for a
cumbersome backstitching mechanism at the replication fork (see Figure
6–13). A hypothetical DNA polymerase that synthesized in the 3ʹ-to-5ʹ
direction (and would thereby circumvent the need for backstitching)
would be unable to proofread: if it removed an incorrectly paired nucleotide, the polymerase would create a chemical dead end—a chain that
could no longer be elongated. Thus, for a DNA polymerase to function
as a self-correcting enzyme that removes its own polymerization errors
as it moves along the DNA, it must proceed only in the 5ʹ-to-3ʹ direction.
Short Lengths of RNA Act as Primers for DNA Synthesis
3′
3′
when DNA polymerase makes a rare mistake and adds the wrong nucleotide, it can correct the error through an activity called proofreading.
5′
SYNTHESIS CONTINUES IN
THE 5′-TO-3′ DIRECTION
Figure 6–14 During DNA synthesis, DNA
polymerase proofreads its own work. If an
incorrect nucleotide is added to a growing
strand, the DNA polymerase cleaves it from
the strand and replaces it with the correct
nucleotide before continuing.
ECB4 e6.13/6.14
Figure 6–15 DNA polymerase contains
separate sites for DNA synthesis and
proofreading. The diagrams are based on
the structure of an E. coli DNA polymerase
molecule, as determined by X-ray
crystallography. DNA polymerase is shown
with the replicating DNA molecule and the
polymerase in the polymerizing mode (left)
and in the proofreading mode (right). The
catalytic sites for the polymerization activity
(P) and error-correcting proofreading activity
(E) are indicated. When the polymerase
adds an incorrect nucleotide, the newly
synthesized DNA strand (red ) transiently
unpairs from the template strand (orange),
and its growing 3ʹ end moves into the errorcorrecting catalytic site (E) to be removed.
We have seen that the accuracy of DNA replication depends on the
requirement of the DNA polymerase for a correctly base-paired 3ʹ end
before it can add more nucleotides to a growing DNA strand. How then
can the polymerase begin a completely new DNA strand? To get the
process started, a different enzyme is needed—one that can begin a new
polynucleotide strand simply by joining two nucleotides together without
the need for a base-paired end. This enzyme does not, however, synthesize DNA. It makes a short length of a closely related type of nucleic
acid—RNA (ribonucleic acid)—using the DNA strand as a template. This
short length of RNA, about 10 nucleotides long, is base-paired to the template strand and provides a base-paired 3ʹ end as a starting point for DNA
polymerase. It thus serves as a primer for DNA synthesis, and the enzyme
that synthesizes the RNA primer is known as primase.
Primase is an example of an RNA polymerase, an enzyme that synthesizes
RNA using DNA as a template. A strand of RNA is very similar chemically
to a single strand of DNA except that it is made of ribonucleotide subunits, in which the sugar is ribose, not deoxyribose; RNA also differs from
DNA in that it contains the base uracil (U) instead of thymine (T) (see
Panel 2–6, pp. 76–77). However, because U can form a base pair with
A, the RNA primer is synthesized on the DNA strand by complementary
base-pairing in exactly the same way as is DNA (Figure 6–16).
5′
template
strand
3′
5′
P
P
E
newly
synthesized
DNA
POLYMERIZING
EDITING
E
207
DNA Replication
Figure 6–16 RNA primers are synthesized by an RNA polymerase
called primase, which uses a DNA strand as a template. Like DNA
polymerase, primase works in the 5ʹ-to-3ʹ direction. Unlike DNA
polymerase, however, primase can start a new polynucleotide chain by
joining together two nucleoside triphosphates without the need for
a base-paired 3ʹ end as a starting point. (In this case, ribonucleoside
triphosphates, rather than deoxyribonucleoside triphosphates, provide
the incoming nucleotides.)
For the leading strand, an RNA primer is needed only to start replication at a replication origin; once a replication fork has been established,
the DNA polymerase is continuously presented with a base-paired 3ʹ
end as it tracks along the template strand. But on the lagging strand,
where DNA synthesis is discontinuous, new primers are needed to
keep polymerization going (see Figure 6–13). The movement of the
replication fork continually exposes unpaired bases on the lagging
strand template, and new RNA primers are laid down at intervals along
the newly exposed, single-stranded stretch. DNA polymerase adds a
deoxyribonucleotide to the 3ʹ end of each primer to start a new Okazaki
fragment, and it will continue to elongate this fragment until it runs into
the next RNA primer (Figure 6–17).
DNA strand
3′ HO
Proteins at a Replication Fork Cooperate to Form
a Replication Machine
DNA replication requires the cooperation of a large number of proteins
that act in concert to open up the double helix and synthesize new DNA.
These proteins form part of a remarkably complex replication machine.
The first problem faced by the replication machine is accessing the
Figure 6–17 Multiple enzymes are required to synthesize Okazaki
fragments on the lagging DNA strand. In eukaryotes, RNA primers
are made at intervals of about 200 nucleotides on the lagging strand,
and each RNA primer is approximately 10 nucleotides long. Primers
are removed by nucleases that recognize an RNA strand in an RNA/
DNA helix and degrade it; this leaves gaps that are filled in by a
repair DNA polymerase that can proofread as it fills in the gaps. The
completed fragments are finally joined together by an enzyme called
DNA ligase, which catalyzes the formation of a phosphodiester bond
between the 3ʹ-OH end of one fragment and the 5ʹ-phosphate end of
the next, thus linking up the sugar–phosphate backbones. This nicksealing reaction requires an input of energy in the form of ATP (not
shown; see Figure 6–18).
3′
5′
RNA primer
primase
3′ HO
5′
3′
5′
To produce a continuous new DNA strand from the many separate pieces
of nucleic acid made on the lagging strand, three additional enzymes are
needed. These act quickly to remove the RNA primer, replace it with DNA,
and join the DNA fragments together. Thus, a nuclease degrades the RNA
primer, a DNA polymerase called a repair polymerase then replaces this
RNA with DNA (using the end of the adjacent Okazaki fragment as a
primer), and the enzyme DNA ligase joins the 5ʹ-phosphate end of one
DNA fragment to the adjacent 3ʹ-hydroxyl end of the next (Figure 6–18).
Primase can begin new polynucleotide chains, but this activity is possible
because the enzyme does not proofread its work. As a result, primers frequently contain mistakes. But because primers are made of RNA instead
of DNA, they stand out as “suspect copy” to be automatically removed
and replaced by DNA. The repair DNA polymerases that make this DNA,
like the replicative polymerases, proofread as they synthesize. In this
way, the cell’s replication machinery is able to begin new DNA chains
and, at the same time, ensure that all of the DNA is copied faithfully.
3′
5′
ECB4 m5.11/6.16
previous
Okazaki
fragment old RNA
primer
3′
5′
5′
DNA
laggingstrand
template
3′
5′
new RNA primer
synthesis by
primase
3′
5′
3′
DNA polymerase adds nucleotides
to 3′ end of new RNA primer
to start new Okazaki fragment
5′ 3′
5′
3′
DNA polymerase finishes
DNA fragment
3′
5′
5′
3′
old RNA primer erased
and replaced by DNA
3′
5′
5′
3′
nick sealed by DNA ligase,
joining new Okazaki fragment
to the growing DNA strand
3′
5′
5′
3′
208
Chapter 6
previous
Okazaki
fragment
DNA Replication, Repair, and Recombination
5′ phosphate
new Okazaki
fragment
ATP
3′ OH
A P P P
P Pi
A P
A P
continuous new DNA strand
5′
3′
5′
3′
DNA lagging strand
Figure 6–18 DNA ligase joins together
Okazaki fragments on the lagging strand
during DNA synthesis. The ligase enzyme
uses a molecule of ATP to activate the 5ʹ
end of one fragment (step 1) before forming
a new bond with the 3ʹ end of the other
fragment (step 2).
STEP 1
STEP 2
ATP
used
AMP
released
nucleotides that lie at the center of the helix. For DNA replication to occur,
the double helix must be unzipped ahead of the replication fork so that
the incoming nucleoside triphosphates can form base pairs with each
template strand. Two types of replication proteins—DNA helicases and
single-strand DNA-binding proteins—cooperate to carry out this task. The
helicase sits at the very front of the replication machine where it uses the
energy of ATP hydrolysis to propel itself forward, prying apart the double
helix as it speeds along the DNA (Figure 6–19A and Movie 6.2). Singlestrand DNA-binding proteins cling to the single-stranded DNA exposed
by the helicase, transiently preventing the strands from re-forming base
pairs and keeping them in an elongated form so that they can serve as
efficient templates.
This localized unwinding of the DNA double helix itself presents a prob-
Figure 6–19 DNA synthesis is carried
lem. As the helicase pries open the DNA within the replication fork, the
out by a group of proteins that act
together as a replication machine.
ECB4 m5.13/6.18
(A) DNA polymerases are held on
the leading and lagging strands by
leadingsliding clamp
strand
circular protein clamps that allow the
template
DNA polymerase on
polymerases to slide. On the laggingleading strand
strand template, the clamp detaches
each time the polymerase completes an
newly synthesized
Okazaki fragment. A clamp loader (not
DNA strand
parental
shown) is required to attach a sliding
DNA helix
clamp each time a new Okazaki fragment
is begun. At the head of the fork, a DNA
helicase unwinds the strands of the
parental DNA double helix. Single-strand
RNA primer
DNA helicase
DNA-binding proteins keep the DNA
DNA primase
strands apart to provide access for the
new Okazaki fragment
primase and polymerase. For simplicity, previous
next Okazaki fragment
will start here
this diagram shows the proteins working Okazaki
lagging-strand
fragment
independently; in the cell, they are held
template
single-strand DNAtogether in a large replication machine,
binding protein
as shown in (B).
(B) This diagram shows a current view of
DNA polymerase on lagging strand
(just finishing an Okazaki fragment)
how the replication proteins are arranged
(A)
when a replication fork is moving. To
generate this structure, the lagging
newly
strand shown in (A) has been folded to
synthesized
bring its DNA polymerase in contact with
DNA strand
the leading-strand DNA polymerase. This
folding process also brings the 3ʹ end
leadingof each completed Okazaki fragment
strand
close to the start site for the next Okazaki
template
parental
fragment. Because the lagging-strand
DNA helix
DNA polymerase is bound to the rest
of the replication proteins, it can be
reused to synthesize successive Okazaki
fragments; in this diagram, the lagginglagging-strand
template
strand DNA polymerase is about to let go
of its completed Okazaki fragment and
DNA polymerase
move to the RNA primer that is being
RNA
on lagging strand
synthesized by the nearby primase. To
primer new Okazaki (just finishing an
previous
watch the replication complex in action,
fragment
Okazaki fragment) Okazaki
(B)
see Movies 6.4 and 6.5.
fragment
DNA Replication
leading-strand
template
5′
5′
3′
3′
lagging-strand
template
DNA helicase
(A) in the absence of topoisomerase, the DNA cannot
rapidly rotate, and torsional stress builds up
5′
DNA supercoils
caused by
torsional stress
Figure 6–20 DNA topoisomerases
relieve the tension that builds up in
front of a replication fork. (A) As DNA
helicase unwinds the DNA double helix,
it generates a section of overwound
DNA. Tension builds up because the
chromosome is too large to rotate fast
enough to relieve the buildup of torsional
stress. The broken bars in the left-hand
panel represent approximately 20 turns
of DNA. (B) DNA topoisomerases relieve
this stress by generating temporary nicks
in the DNA.
DNA topoisomerase creates transient
single-strand break
3′
(B) free rotation of double helix about phosphodiester
bond relieves torsional stress ahead of helicase,
after which single-strand break is sealed
Question 6–2
DNA on the other side of the fork gets wound more tightly. This excess
twisting in front of the replication fork creates tension in the DNA that—if
allowed to build—makes unwinding the double helix increasingly difficult and impedes the forward movement
of the replication machinery
ECB4 m5.21/6.20
(Figure 6–20A). Cells use proteins called DNA topoisomerases to relieve
this tension. These enzymes produce transient nicks in the DNA backbone, which temporarily release the tension; they then reseal the nick
before falling off the DNA (Figure 6–20B).
An additional replication protein, called a sliding clamp, keeps DNA
polymerase firmly attached to the template while it is synthesizing new
strands of DNA. Left on their own, most DNA polymerase molecules will
synthesize only a short string of nucleotides before falling off the DNA
template strand. The sliding clamp forms a ring around the newly formed
DNA double helix and, by tightly gripping the polymerase, allows the
enzyme to move along the template strand without falling off as it synthesizes new DNA (see Figure 6–19A and Movie 6.3).
Assembly of the clamp around DNA requires the activity of another replication protein, the clamp loader, which hydrolyzes ATP each time it locks
a sliding clamp around a newly formed DNA double helix. This loading
needs to occur only once per replication cycle on the leading strand; on
the lagging strand, however, the clamp is removed and then reattached
each time a new Okazaki fragment is made.
Most of the proteins involved in DNA replication are held together in
a large multienzyme complex that moves as a unit along the parental
DNA double helix, enabling DNA to be synthesized on both strands in a
coordinated manner. This complex can be likened to a miniature sewing
machine composed of protein parts and powered by nucleoside triphosphate hydrolysis (Figure 6–19B and Movies 6.4 and 6.5).
Telomerase Replicates the Ends of Eukaryotic
Chromosomes
Having discussed how DNA replication begins at origins and how movement of a replication fork proceeds, we now turn to the special problem
209
Discuss the following statement:
“Primase is a sloppy enzyme that
makes many mistakes. Eventually,
the RNA primers it makes are
disposed of and replaced with DNA
synthesized by a polymerase with
higher fidelity. This is wasteful. It
would be more energy-efficient if a
DNA polymerase made an accurate
copy in the first place.”
210
Chapter 6
DNA Replication, Repair, and Recombination
5′
3′
lagging strand
RNA primers
5′
3′
3′
5′
3′
5′
chromosome
end
leading strand
REPLICATION FORK REACHES
END OF CHROMOSOME
lagging strand
leading strand
RNA PRIMERS REPLACED BY DNA;
GAPS SEALED BY LIGASE
lagging strand
gap remaining at
end of lagging
strand
leading strand
Figure 6–21 Without a special mechanism to replicate the ends of linear
chromosomes, DNA would be lost during each round of cell division. DNA
synthesis begins at origins of replication and continues until the replication
machinery reaches the ends of the chromosome. The leading strand is reproduced in
its entirety. But the ends of the lagging strand can’t be completed, because once the
final RNA primer has been removed there is no way to replace it with DNA. These
gaps at the ends of the lagging strand must be filled in by a special mechanism to
keep the chromosome endsECB4
from N6.101/6.21
shrinking with each cell division.
Question 6–3
A gene encoding one of the proteins
involved in DNA replication has
been inactivated by a mutation in a
cell. In the absence of this protein,
the cell attempts to replicate its
DNA. What would happen during
the DNA replication process if
each of the following proteins were
missing?
A.DNA polymerase
B. DNA ligase
C. Sliding clamp for DNA
polymerase
D. Nuclease that removes RNA
primers
E.DNA helicase
F. Primase
of replicating the very ends of chromosomes. As we discussed previously, because DNA replication proceeds only in the 5ʹ-to-3ʹ direction,
the lagging strand of the replication fork has to be synthesized in the
form of discontinuous DNA fragments, each of which is primed with an
RNA primer laid down by a primase (see Figure 6–17). A serious problem
arises, however, as the replication fork approaches the end of a chromosome: although the leading strand can be replicated all the way to the
chromosome tip, the lagging strand cannot. When the final RNA primer
on the lagging strand is removed, there is no way to replace it (Figure
6–21). Without a strategy to deal with this problem, the lagging strand
would become shorter with each round of DNA replication; after repeated
cell divisions, chromosomes would shrink—and eventually lose valuable
genetic information.
Bacteria solve this “end-replication” problem by having circular DNA
molecules as chromosomes. Eukaryotes solve it by having long, repetitive nucleotide sequences at the ends of their chromosomes which are
incorporated into structures called telomeres. These telomeric DNA
sequences attract an enzyme called telomerase to the chromosome
ends. Using an RNA template that is part of the enzyme itself, telomerase
extends the ends of the replicating lagging strand by adding multiple copies of the same short DNA sequence to the template strand. This extended
template allows replication of the lagging strand to be completed by conventional DNA replication (Figure 6–22).
In addition to allowing replication of chromosome ends, telomeres form
structures that mark the true ends of a chromosome. This allows the cell
to distinguish unambiguously between the natural ends of chromosomes
and the double-strand DNA breaks that sometimes occur accidentally in
DNA Repair
end of
chromosome
telomere repeat sequence
3′
TELOMERASE
BINDS TO
TEMPLATE STRAND
TELOMERASE ADDS
ADDITIONAL TELOMERE
REPEATS TO TEMPLATE
STRAND (RNA-TEMPLATED
DNA SYNTHESIS)
COMPLETION OF LAGGING
STRAND BY DNA
POLYMERASE (DNATEMPLATED DNA SYNTHESIS)
template of lagging strand
5′ incomplete, newly synthesized lagging strand
3′
5′
direction of
telomere
DNA synthesis
5′
3′
telomerase with its bound RNA template
3′
5′
5′
3′
extended template strand
3′
DNA
polymerase
5′
the middle of chromosomes. These breaks are dangerous and must be
immediately repaired, as we see in the next section.
DNA Repair
The diversity of living organisms and their success in colonizing almost
ECB4 depend
e6.18/6.22
every part of the Earth’s surface
on genetic changes accumulated
gradually over millions of years. Some of these changes allow organisms
to adapt to changing conditions and to thrive in new habitats. However,
in the short term, and from the perspective of an individual organism,
genetic alterations can be detrimental. In a multicellular organism, such
permanent changes in the DNA—called mutations—can upset the organism’s extremely complex and finely tuned development and physiology.
To survive and reproduce, individuals must be genetically stable. This
stability is achieved not only through the extremely accurate mechanism
for replicating DNA that we have just discussed, but also through the
work of a variety of protein machines that continually scan the genome
for damage and fix it when it occurs. Although some changes arise from
rare mistakes in the replication process, the majority of DNA damage is
an unintended consequence of the vast number of chemical reactions
that occur inside cells.
Most DNA damage is only temporary, because it is immediately corrected
by processes collectively called DNA repair. The importance of these DNA
repair processes is evident from the consequences of their malfunction.
Humans with the genetic disease xeroderma pigmentosum, for example,
cannot mend the damage done by ultraviolet (UV) radiation because they
have inherited a defective gene for one of the proteins involved in this
repair process. Such individuals develop severe skin lesions, including
skin cancer, because of the accumulation of DNA damage in cells that
are exposed to sunlight and the consequent mutations that arise in these
cells.
In this section, we describe a few of the specialized mechanisms cells
use to repair DNA damage. We then consider examples of what happens
when these mechanisms fail—and discuss how the fidelity of DNA replication and repair are reflected in our genome.
211
Figure 6–22 Telomeres and telomerase
prevent linear eukaryotic chromosomes
from shortening with each cell division.
For clarity, only the template DNA (orange)
and newly synthesized DNA (red) of the
lagging strand are shown (see bottom of
Figure 6–21). To complete the replication
of the lagging strand at the ends of a
chromosome, the template strand is first
extended beyond the DNA that is to
be copied. To achieve this, the enzyme
telomerase adds more repeats to the
telomere repeat sequences at the 3ʹ end of
the template strand, which then allows the
lagging strand to be completed by DNA
polymerase, as shown. The telomerase
enzyme carries a short piece of RNA (blue)
with a sequence that is complementary to
the DNA repeat sequence; this RNA acts as
the template for telomere DNA synthesis.
After the lagging-strand replication
is complete, a short stretch of singlestranded DNA remains at the ends of the
chromosome, as shown. To see telomerase
in action, view Movie 6.6.
212
Chapter 6
DNA Replication, Repair, and Recombination
Figure 6–23 Depurination and
deamination are the most frequent
chemical reactions known to create
serious DNA damage in cells.
(A) Depurination can remove guanine
(or adenine) from DNA. (B) The major
type of deamination reaction converts
cytosine to an altered DNA base, uracil;
however, deamination can also occur on
other bases as well. Both depurination and
deamination take place on double-helical
DNA, and neither break the phosphodiester
backbone.
(A) DEPURINATION
O
N
N
H
N
PP
N
H2O
H
N
PP
OH
sugar phosphate
after depurination
O
GUANINE H
O
O
H
N
N
H
N
DNA strand
N
H
H
N
DNA strand
H
H
GUANINE
(B) DEAMINATION
CYTOSINE
H
N
H
H
PP
URACIL
H
H2O
O
H
N
H
O
N
NH3
PP
O
N
H
O
N
O
DNA Damage Occurs Continually in Cells
Just like any other molecule in the cell, DNA is continually undergoing
thermal collisions with other molecules, often resulting in major chemical changes in the DNA. For example, during the time it takes to read
this sentence, a total of about a trillion (1012) purine bases (A and G)
will be lost from DNA in the cells of your body by a spontaneous reaction called depurination (Figure 6–23A). Depurination does not break the
ECB4
m5.45/6.28
DNA phosphodiester
backbone
but instead removes a purine base from a
nucleotide, giving rise to lesions that resemble missing teeth (see Figure
6–25B). Another common reaction is the spontaneous loss of an amino
group (deamination) from a cytosine in DNA to produce the base uracil
(Figure 6–23B). Some chemically reactive by-products of cell metabolism
also occasionally react with the bases in DNA, altering them in such a
way that their base-pairing properties are changed.
Question 6–4
Discuss the following statement:
“The DNA repair enzymes that
fix deamination and depurination
damage must preferentially
recognize such damage on newly
synthesized DNA strands.”
The ultraviolet radiation in sunlight is also damaging to DNA; it promotes
covalent linkage between two adjacent pyrimidine bases, forming, for
example, the thymine dimer shown in Figure 6–24. It is the failure to
repair thymine dimers that spells trouble for individuals with the disease
xeroderma pigmentosum.
THYMINE
P
O
O
P
H
N
C
N
Figure 6–24 The ultraviolet radiation
in sunlight can cause the formation of
thymine dimers. Two adjacent thymine
bases have become covalently attached
to each other to form a thymine dimer.
Skin cells that are exposed to sunlight
are especially susceptible to this type of
DNA damage.
P
C
C
H
O
O
CH3
H
N
C
C
H
O
C
N
C
O
C
THYMINE
O
CH3
O
H
N
C
N
UV radiation
P
O
O
C
H
C
C
N
C
H
H
N
O
C
CH3
O
C
C
CH3
THYMINE DIMER
DNA Repair
213
mutated
mutated
old strand
old strand
U
A
deaminated C
depurinated A
new strand
new strand
5′
U
G
3′
3′
5′
an A-T nucleotide
pair has been deleted
a G has been
changed to an A
T
DNA
REPLICATION
DNA
REPLICATION
new strand
C
A
G
T
old strand
old strand
(A)
new strand
unchanged
(B)
These are only a few of many chemical changes that can occur in our
DNA. If left unrepaired, many of them would lead either to the substitution of one nucleotide pair for another as a result of incorrect base-pairing
during replication (Figure 6–25A) or to deletion of one or more nucleotide
pairs in the daughter DNA strand after DNA replication (Figure 6–25B).
Some types of DNA damage (thymine dimers, for example) can stall the
DNA replication machinery at the site of the damage.
In addition to this chemical damage, DNA can also be altered by replication itself. The replication machinery that copies the DNA can—quite
rarely—incorporate an incorrect nucleotide that it fails to correct via
proofreading (see Figure 6–14).
For each of these forms of DNA, cells possess ECB4
a mechanism
for repair, as
e6.25/6.30
we discuss next.
Cells Possess a Variety of Mechanisms for Repairing DNA
The thousands of random chemical changes that occur every day in the
DNA of a human cell—through thermal collisions or exposure to reactive metabolic by-products, DNA-damaging chemicals, or radiation—are
repaired by a variety of mechanisms, each catalyzed by a different set
of enzymes. Nearly all these repair mechanisms depend on the double-helical structure of DNA, which provides two copies of the genetic
information—one in each strand of the double helix. Thus, if the sequence
in one strand is accidentally damaged, information is not lost irretrievably, because a backup version of the altered strand remains in the
complementary sequence of nucleotides in the other strand. Most DNA
damage creates structures that are never encountered in an undamaged
DNA strand; thus the good strand is easily distinguished from the bad.
The basic pathway for repairing damage to DNA, illustrated schematically
in Figure 6–26, involves three basic steps:
1. The damaged DNA is recognized and removed by one of a variety
of mechanisms. These involve nucleases, which cleave the covalent bonds that join the damaged nucleotides to the rest of the DNA
strand, leaving a small gap on one strand of the DNA double helix
in the region.
2. A repair DNA polymerase binds to the 3ʹ-hydroxyl end of the cut
DNA strand. It then fills in the gap by making a complementary
copy of the information stored in the undamaged strand. Although
unchanged
Figure 6–25 Chemical modifications of
nucleotides, if left unrepaired, produce
mutations. (A) Deamination of cytosine,
if uncorrected, results in the substitution
of one base for another when the DNA
is replicated. As shown in Figure 6–23B,
deamination of cytosine produces uracil.
Uracil differs from cytosine in its basepairing properties and preferentially
base-pairs with adenine. The DNA
replication machinery therefore inserts
an adenine when it encounters a uracil
on the template strand. (B) Depurination,
if uncorrected, can lead to the loss of
a nucleotide pair. When the replication
machinery encounters a missing purine
on the template strand, it can skip to the
next complete nucleotide, as shown, thus
producing a daughter DNA molecule that
is missing one nucleotide pair. In other
cases (not shown), the replication machinery
places an incorrect nucleotide across from
the missing base, again resulting in a
mutation.
214
Chapter 6
DNA Replication, Repair, and Recombination
5′
3′
3′
5′
DAMAGE TO
TOP STRAND
step 1
step 2
EXCISION OF
SEGMENT OF
DAMAGED STRAND
REPAIR DNA POLYMERASE
FILLS IN MISSING
NUCLEOTIDES IN
TOP STRAND USING
BOTTOM STRAND AS
A TEMPLATE
different from the DNA polymerase that replicates DNA, repair
DNA polymerases synthesize DNA strands in the same way. For
example, they elongate chains in the 5ʹ-to-3ʹ direction and have
the same type of proofreading activity to ensure that the template
strand is copied accurately. In many cells, this is the same enzyme
that fills in the gap left after the RNA primers are removed during
the normal DNA replication process (see Figure 6–17).
3. When the repair DNA polymerase has filled in the gap, a break
remains in the sugar–phosphate backbone of the repaired strand.
This nick in the helix is sealed by DNA ligase, the same enzyme
that joins the Okazaki fragments during replication of the lagging
DNA strand.
Steps 2 and 3 are nearly the same for most types of DNA damage,
including the rare errors that arise during DNA replication. However,
step 1 uses a series of different enzymes, each specialized for removing
different types of DNA damage. Humans produce hundreds of different
proteins that function in DNA repair.
A DNA Mismatch Repair System Removes Replication
Errors That Escape Proofreading
step 3
DNA LIGASE
SEALS NICK
NET RESULT: REPAIRED DNA
Figure 6–26 The basic mechanism of
DNA repair involves three steps. In step 1
(excision), the damage is cut out by one of
a series of nucleases, each specialized for a
type of DNA
In step 2 (resynthesis),
ECB4damage.
e6.26/6.25
the original DNA sequence is restored by
a repair DNA polymerase, which fills in the
gap created by the excision events. In step
3 (ligation), DNA ligase seals the nick left
in the sugar–phosphate backbone of the
repaired strand. Nick sealing, which requires
energy from ATP hydrolysis, remakes the
broken phosphodiester bond between the
adjacent nucleotides (see Figure 6–18).
Although the high fidelity and proofreading abilities of the cell’s replication machinery generally prevent replication errors from occurring, rare
mistakes do happen. Fortunately, the cell has a backup system—called
mismatch repair—which is dedicated to correcting these errors. The
replication machine makes approximately one mistake per 107 nucleotides copied; DNA mismatch repair corrects 99% of these replication
errors, increasing the overall accuracy to one mistake in 109 nucleotides
copied. This level of accuracy is much, much higher than that generally
encountered in our day-to-day lives (Table 6–1).
Whenever the replication machinery makes a copying mistake, it leaves
behind a mispaired nucleotide (commonly called a mismatch). If left
uncorrected, the mismatch will result in a permanent mutation in the
next round of DNA replication (Figure 6–27). A complex of mismatch
repair proteins recognizes such a DNA mismatch, removes a portion of
the DNA strand containing the error, and then resynthesizes the missing
DNA. This repair mechanism restores the correct sequence (Figure 6–28).
To be effective, the mismatch repair system must be able to recognize
which of the DNA strands contains the error. Removing a segment
from the strand of DNA that contains the correct sequence would only
Table 6–1 Error Rates
US Postal Service on-time delivery of local
first-class mail
13 late deliveries per 100 parcels
Airline luggage system
1 lost bag per 150
A professional typist typing at 120 words
per minute
1 mistake per 250 characters
Driving a car in the United States
1 death per 104 people per year
DNA replication (without proofreading)
1 mistake per 105 nucleotides
copied
DNA replication (with proofreading;
without mismatch repair)
1 mistake per 107 nucleotides
copied
DNA replication (with mismatch repair)
1 mistake per 109 nucleotides
copied
DNA Repair
TOP STRAND
REPLICATED
CORRECTLY
215
original parent strand
C
G
parent DNA
molecule
5′
3′
C
G
new strand
3′
strand with error
REPLICATION
5′
MUTATED
DNA
MOLECULE
A
MISTAKE
OCCURS DURING
REPLICATION OF
BOTTOM STRAND
T
new strand with error REPLICATION
WITHOUT
REPAIR
A
G
newly synthesized
strand
newly synthesized
strand
original parent strand
NORMAL
DNA
MOLECULE
C
compound the mistake. The way the mismatch system solves this problem is by always removing a portion of the newly made DNA strand. In
bacteria, newly synthesized DNA lacks a type of chemical modification
that is present on the preexisting parent DNA. Other cells use other strategies for distinguishing their parent DNA from a newly replicated strand.
Mismatch repair plays an important role in preventing cancer. An inherited predisposition to certain cancers (especially some types of colon
cancer) is caused by mutations in genes that encode mismatch repair
proteins. Humans inherit two copies of these genes (one from each parent), and individuals who inherit one damaged mismatch repair gene
are unaffected until the undamaged copy of the same gene is randomly
mutated in a somatic cell. This mutant cell—and all of its progeny—are
ECB4 n6.102/6.26
then deficient in mismatch repair; they therefore accumulate mutations
more rapidly than do normal cells. Because cancers arise from cells that
have accumulated multiple mutations, a cell deficient in mismatch repair
has a greatly enhanced chance of becoming cancerous. Thus, inheriting
a damaged mismatch repair gene strongly predisposes an individual to
cancer.
G
original parent strand
Figure 6–27 Errors made during DNA
replication must be corrected to avoid
mutations. If uncorrected, a mismatch will
lead to a permanent mutation in one of the
two DNA molecules produced by the next
round of DNA replication.
Double-Strand DNA Breaks Require a Different Strategy
for Repair
The repair mechanisms we have discussed thus far rely on the genetic
redundancy built into every DNA double helix. If nucleotides on one
strand are damaged, they can be repaired using the information present
in the complementary strand.
But what happens when both strands of the double helix are damaged
at the same time? Radiation, mishaps at the replication fork, and various chemical assaults can all fracture the backbone of DNA, creating a
TOP STRAND
REPLICATED
CORRECTLY
original parent strand
C
G
parent DNA
molecule
5′
3′
C
G
new strand
3′
5′
REPLICATION
MISTAKE
OCCURS DURING
REPLICATION OF
BOTTOM STRAND
new strand with error
A
G
original parent strand
Figure 6–28 Mismatch repair eliminates
replication errors and restores the
original DNA sequence. When mistakes
occur during DNA replication, the repair
machinery must replace the incorrect
nucleotide on the newly synthesized strand,
using the original parent strand as its
template. This mechanism eliminates the
mutation.
MISMATCH
REPAIR
C
G
ORIGINAL
STRAND
RESTORED
216
Chapter 6
DNA Replication, Repair, and Recombination
Figure 6–29 Cells can repair
double-strand breaks in one of
two ways. (A) In nonhomologous
end joining, the break is first
“cleaned” by a nuclease that
chews back the broken ends
to produce flush ends. The
flush ends are then stitched
together by a DNA ligase. Some
nucleotides are lost in the repair
process, as indicated by the black
lines in the repaired DNA. (B) If
a double-strand break occurs in
one of two daughter DNA double
helices after DNA replication
has occurred, but before the
daughter chromosomes have
been separated, the undamaged
double helix can be readily
used as a template to repair
the damaged double helix by
homologous recombination. This
is a more involved process than
non-homologous end joining, but
it accurately restores the original
DNA sequence at the site of the
break. The detailed mechanism is
presented in Figure 6–30.
(A) NONHOMOLOGOUS END JOINING
(B) HOMOLOGOUS RECOMBINATION
accidental double-strand break
3′
5′
5′
3′
PROCESSING OF
DNA END BY
NUCLEASE
END JOINING
BY DNA LIGASE
5′
3′
3′
5′
3′
5′
5′
3′
damaged
DNA molecule homologous
DNA
undamaged
molecules
DNA molecule
PROCESSING OF BROKEN ENDS
BY SPECIAL NUCLEASE
DOUBLE-STRAND BREAK ACCURATELY
REPAIRED USING UNDAMAGED DNA
AS TEMPLATE
deletion of DNA sequence
BREAK REPAIRED WITH SOME
LOSS OF NUCLEOTIDES AT
REPAIR SITE
BREAK REPAIRED WITH NO
LOSS OF NUCLEOTIDES AT
REPAIR SITE
double-strand
break. Such lesions are particularly dangerous, because
ECB4 m5.51/6.31
they can lead to the fragmentation of chromosomes and the subsequent
loss of genes.
This type of damage is especially difficult to repair. Each chromosome
contains unique information; if a chromosome undergoes a doublestrand break, and the broken pieces become separated, the cell has no
spare copy it can use to reconstruct the information that is now missing.
To handle this potentially disastrous type of DNA damage, cells have
evolved two basic strategies. The first involves rapidly sticking the broken
ends back together, before the DNA fragments drift apart and get lost.
This repair mechanism, called nonhomologous end joining, occurs in
many cell types and is carried out by a specialized group of enzymes that
“clean” the broken ends and rejoin them by DNA ligation. This “quick and
dirty” mechanism rapidly repairs the damage, but it comes with a price:
in “cleaning” the break to make it ready for ligation, nucleotides are often
lost at the site of repair (Figure 6–29A).
In most cases, this emergency repair mechanism mends the damage
without creating any additional problems. But if the imperfect repair disrupts the activity of a gene, the cell could suffer serious consequences.
Thus, nonhomologous end joining can be a risky strategy for fixing
broken chromosomes. So cells have an alternative, error-free strategy
for repairing double-strand breaks, called homologous recombination
(Figure 6–29B), as we discuss next.
Homologous Recombination Can Flawlessly Repair DNA
Double-Strand Breaks
The problem with repairing a double-strand break, as we mentioned,
is finding an intact template to guide the repair. However, if a doublestrand break occurs in one double helix shortly after a stretch of DNA
has been replicated, the undamaged double helix can readily serve as
a template to guide the repair of the broken DNA: information on the
undamaged strand of the intact double helix is used to repair the complementary broken strand in the other. Because the two DNA molecules
DNA Repair
217
are homologous—they have identical nucleotide sequences outside the
broken region—this mechanism is known as homologous recombination. It results in a flawless repair of the double-strand break, with no loss
of genetic information (see Figure 6–29B).
Homologous recombination most often occurs shortly after a cell’s DNA
has been replicated before cell division, when the duplicated helices are
still physically close to each other (Figure 6–30A). To initiate the repair, a
nuclease chews back the 5ʹ ends of the two broken strands at the break
(Figure 6–30B). Then, with the help of specialized enzymes, one of the
broken 3ʹ ends “invades” the unbroken homologous DNA duplex and
searches for a complementary sequence through base-pairing (Figure
6–30C). Once an extensive, accurate match is found, the invading strand
is elongated by a repair DNA polymerase, using the complementary strand
as a template (Figure 6–30D). After the repair polymerase has passed
the point where the break occurred, the newly repaired strand rejoins
its original partner, forming base pairs that hold the two strands of the
broken double helix together (Figure 6–30E). Repair is then completed
by additional DNA synthesis at the 3ʹ ends of both strands of the broken
double helix (Figure 6–30F), followed by DNA ligation (Figure 6–30G).
(A)
double-strand break
5′
3′
3′
5′
3′
5′
5′
3′
NUCLEASE DIGESTS 5′ ENDS
OF BROKEN STRANDS
(B)
5′
3′
5′
3′
3′
5′
3′
5′
5′
3′
3′
5′
STRAND INVASION BY
COMPLEMENTARY BASE-PAIRING
(C)
5′
3′
daughter DNA
molecules
5′
3′
5′
3′
5′
(D)
5′
3′
5′
REPAIR POLYMERASE SYNTHESIZES DNA (GREEN)
USING UNDAMAGED COMPLEMENTARY DNA AS TEMPLATE
3′
5′
3′
5′
(E)
5′
3′
INVADING STRAND RELEASED; BROKEN
DOUBLE HELIX RE-FORMED
5′
5′
3′
5′
(F)
5′
3′
DNA SYNTHESIS CONTINUES USING COMPLEMENTARY STRANDS
FROM DAMAGED DNA AS TEMPLATE
3′
5′
(G)
DNA LIGATION
5′
3′
3′
5′
DOUBLE-STRAND BREAK IS
ACCURATELY REPAIRED
Figure 6–30 Homologous recombination
allows the flawless repair of DNA doublestrand breaks. This is the preferred method
for repairing double-strand breaks that arise
shortly after the DNA has been replicated
but before the cell has divided. See text
for details. (Adapted from M. McVey et al.,
Proc. Natl. Acad. Sci. USA 101:15694–15699,
2004. With permission from the National
Academy of Sciences.)
218
Chapter 6
DNA Replication, Repair, and Recombination
The net result is two intact DNA helices, where the genetic information
from one was used as a template to repair the other.
Homologous recombination can also be used to repair many other types
of DNA damage, making it perhaps the most handy DNA repair mechanism available to the cell: all that is needed is an intact homologous
chromosome to use as a partner—a situation that occurs transiently each
time a chromosome is duplicated. The “all-purpose” nature of homologous recombinational repair probably explains why this mechanism, and
the proteins that carry it out, have been conserved in virtually all cells on
Earth.
single DNA strand of
normal β-globin gene
G T G C A C C T G A C T C C T G A G G A G --G T G C A C C T G A C T C C T G T G G A G --single DNA strand of
mutant β-globin gene
single nucleotide
changed (mutation)
(A)
(B)
(C)
5 µm
5 µm
Figure 6–31 A single nucleotide change
causes the disease sickle-cell anemia.
(A) β-globin is one of the two types of
protein subunits that form hemoglobin (see
Figure 4–24). A single nucleotide change
(mutation) in the β-globin gene produces
ECB4that
e6.19/6.23
a β-globin subunit
differs from normal
β-globin only by a change from glutamic
acid to valine at the sixth amino acid
position. (Only a small portion of the gene
is shown here; the β-globin subunit contains
a total of 146 amino acids.) Humans carry
two copies of each gene (one inherited from
each parent); a sickle-cell mutation in one of
the two β-globin genes generally causes no
harm to the individual, as it is compensated
for by the normal gene. However, an
individual who inherits two copies of the
mutant β-globin gene will have sickle-cell
anemia. Normal red blood cells are shown
in (B), and those from an individual suffering
from sickle-cell anemia in (C). Although
sickle-cell anemia can be a life-threatening
disease, the mutation responsible can also
be beneficial. People with the disease,
or those who carry one normal gene and
one sickle-cell gene, are more resistant to
malaria than unaffected individuals, because
the parasite that causes malaria grows
poorly in red blood cells that contain the
sickle-cell form of hemoglobin.
Homologous recombination is versatile, and has a crucial role in the
exchange of genetic information during the formation of the germ cells—
sperm and eggs. This specialized process, called meiosis, enhances the
generation of genetic diversity within a species during sexual reproduction. We will discuss it when we talk about sex in Chapter 19.
Failure to Repair DNA Damage Can Have Severe
Consequences for a Cell or Organism
On occasion, the cell’s DNA replication and repair processes fail and give
rise to a mutation. This permanent change in the DNA sequence can have
profound consequences. A mutation that affects just a single nucleotide
pair can severely compromise an organism’s fitness if the change occurs
in a vital position in the DNA sequence. Because the structure and activity of each protein depend on its amino acid sequence, a protein with an
altered sequence may function poorly or not at all. For example, humans
use the protein hemoglobin to transport oxygen in the blood (see Figure
4–24). A permanent change in a single nucleotide in a hemoglobin gene
can cause cells to make hemoglobin with an incorrect sequence of amino
acids. One such mutation causes the disease sickle-cell anemia. The
sickle-cell hemoglobin is less soluble than normal hemoglobin and forms
fibrous intracellular precipitates, which produce the characteristic sickle
shape of affected red blood cells (Figure 6–31). Because these cells are
more fragile and frequently tear as they travel through the bloodstream,
patients with this potentially life-threatening disease have fewer red blood
cells than usual—that is, they are anemic. This anemia can cause weakness, dizziness, headaches, and breathlessness. Moreover, the abnormal
red blood cells can aggregate and block small vessels, causing pain and
organ failure. We know about sickle-cell hemoglobin because individuals with the mutation survive; the mutation even provides a benefit—an
increased resistance to malaria. Over the course of evolution, many other
mutations in the hemoglobin gene have arisen, but only those that do not
completely destroy the protein remain in the population.
The example of sickle-cell anemia, which is an inherited disease, illustrates the importance of protecting reproductive cells (germ cells) against
mutation. A mutation in a germ cell will be passed on to all the cells in
the body of the multicellular organism that develops from it, including the
germ cells responsible for the production of the next generation.
The many other cells in a multicellular organism (its somatic cells) must
also be protected against mutation—in this case, against mutations that
arise during the life of an individual. Nucleotide changes that occur in
somatic cells can give rise to variant cells, some of which grow and
divide in an uncontrolled fashion at the expense of the other cells in the
organism. In the extreme case, an unchecked cell proliferation known
as cancer results. Cancers are responsible for about 30% of the deaths
that occur in Europe and North America, and they are caused largely by
a gradual accumulation of random mutations in a somatic cell and its
219
DNA Repair
descendants (Figure 6–32). Increasing the mutation frequency even twoor threefold could cause a disastrous increase in the incidence of cancer
by accelerating the rate at which such somatic cell variants arise.
Thus, the high fidelity with which DNA sequences are replicated and
maintained is important both for reproductive cells, which transmit the
genes to the next generation, and for somatic cells, which normally function as carefully regulated members of the complex community of cells
in a multicellular organism. We should therefore not be surprised to find
that all cells possess a very sophisticated set of mechanisms to reduce
the number of mutations that occur in their DNA, devoting hundreds of
genes to these repair processes.
180
160
incidence of colon cancer per 100,000 women
Figure 6–32 Cancer incidence increases dramatically with age. The
number of newly diagnosed cases of cancer of the colon in women
in England and Wales in one year is plotted as a function of age at
diagnosis. Colon cancer, like most human cancers, is caused by the
accumulation of multiple mutations. Because cells are continually
experiencing accidental changes to their DNA—which accumulate and
are passed on to progeny cells when the mutated cells divide—the
chance that a cell will become cancerous increases greatly with age.
(Data from C. Muir et al., Cancer Incidence in Five Continents, Vol. V.
Lyon: International Agency for Research on Cancer, 1987.)
140
120
100
80
60
40
20
0
10
20
30 40 50
age (years)
60
70
80
A Record of the Fidelity of DNA Replication and Repair Is
Preserved in Genome Sequences
Although the majority of mutations do neither harm nor good to an
organism, those that have harmful consequences are usually eliminated
from the population through natural selection; individuals carrying the
altered DNA may die or experience decreased fertility, in which case
these changes will be lost. By contrast, favorable changes will tend to
persist and spread.
ECB4 e6.20/6.24
But even where no selection operates—at the many sites in the DNA
where a change of nucleotide has no effect on the fitness of the organism—the genetic message has been faithfully preserved over tens of
millions of years. Thus humans and chimpanzees, after about 5 million
years of divergent evolution, still have DNA sequences that are at least
98% identical. Even humans and whales, after 10 or 20 times this amount
of time, have chromosomes that are unmistakably similar in their DNA
sequence, and many proteins have amino acid sequences that are almost
identical (Figure 6–33). Thus our genome—and those of our relatives—
contains a message from the distant past. Thanks to the faithfulness of
DNA replication and repair, 100 million years of evolution have scarcely
changed its essential content.
whale
human
Figure 6–33 The sex-determination
genes from humans and whales are
unmistakably similar. Although their body
plans are strikingly different, humans and
whales are built from the same proteins.
Despite the many millions of years that
have passed since humans and whales
diverged, the nucleotide sequences of
many of their genes are closely similar. The
DNA sequences of a part of the gene that
determines maleness in humans and in
whales are shown, one above the other; the
positions where the two are identical are
shaded in green.
220
Chapter 6
DNA Replication, Repair, and Recombination
Essential Concepts
•
Before a cell divides, it must accurately replicate the vast quantity of
genetic information carried in its DNA.
•
Because the two strands of a DNA double helix are complementary,
each strand can act as a template for the synthesis of the other. Thus
DNA replication produces two identical, double-helical DNA molecules, enabling genetic information to be copied and passed on from
a cell to its daughter cells and from a parent to its offspring.
•
During replication, the two strands of a DNA double helix are pulled
apart at a replication origin to form two Y-shaped replication forks.
DNA polymerases at each fork produce a new complementary DNA
strand on each parental strand.
•
DNA polymerase replicates a DNA template with remarkable fidelity, making only about one error in every 107 nucleotides copied.
This accuracy is made possible, in part, by a proofreading process in
which the enzyme corrects its own mistakes as it moves along the
DNA.
•
Because DNA polymerase synthesizes new DNA in only one direction,
only the leading strand at the replication fork can be synthesized in
a continuous fashion. On the lagging strand, DNA is synthesized in
a discontinuous backstitching process, producing short fragments of
DNA that are later joined together by DNA ligase.
•
DNA polymerase is incapable of starting a new DNA chain from
scratch. Instead, DNA synthesis is primed by an RNA polymerase
called primase, which makes short lengths of RNA primers that are
then elongated by DNA polymerase. These primers are subsequently
erased and replaced with DNA.
•
DNA replication requires the cooperation of many proteins that form
a multienzyme replication machine that copies both DNA strands as
it moves along the double helix.
•
In eukaryotes, a special enzyme called telomerase replicates the
DNA at the ends of the chromosomes.
•
The rare copying mistakes that escape proofreading are dealt with by
mismatch repair proteins, which increase the accuracy of DNA replication to one mistake per 109 nucleotides copied.
•
Damage to one of the two DNA strands, caused by unavoidable
chemical reactions, is repaired by a variety of DNA repair enzymes
that recognize damaged DNA and excise a short stretch of the damaged strand. The missing DNA is then resynthesized by a repair DNA
polymerase, using the undamaged strand as a template.
•
If both DNA strands are broken, the double-strand break can be rapidly repaired by nonhomologous end joining. Nucleotides are lost in
the process, altering the DNA sequence at the repair site.
•
Homologous recombination can flawlessly repair double-strand
breaks using an undamaged homologous double helix as a template.
•
Highly accurate DNA replication and DNA repair processes play a key
role in protecting us from the uncontrolled growth of somatic cells
known as cancer.
221
Chapter 6 End-of-Chapter Questions
Key terms
cancer
nonhomologous end joining
DNA ligaseOkazaki fragment
DNA polymerase
primase
DNA repair
proofreading
DNA replication
replication fork
homologous recombination
replication origin
lagging strandRNA (ribonucleic acid)
leading strand
telomerase
mismatch repair
telomere
mutation
template
Questions
Question 6–5
Question 6–9
DNA mismatch repair enzymes preferentially repair bases
on the newly synthesized DNA strand, using the old DNA
strand as a template. If mismatches were simply repaired
without regard for which strand served as template, would
this reduce replication errors? Explain your answer.
Look carefully at Figure 6–11 and at the structures of the
compounds shown in Figure Q6–9.
Question 6–6
NH2
O
–O
O
P
O–
Suppose a mutation affects an enzyme that is required to
repair the damage to DNA caused by the loss of purine
bases. The loss of a purine occurs about 5000 times in the
DNA of each of your cells per day. As the average difference
in DNA sequence between humans and chimpanzees is
about 1%, how long will it take you to turn into an ape?
What is wrong with this argument?
Question 6–7
O
P
N
O
O
O–
P
OH
O
–O
O
O
P
O–
P
N
O
O
O–
P
The speed of DNA replication at a replication fork is about
100 nucleotides per second in human cells. What is the
minimum number of origins of replication that a human cell
must have if it is to replicate its DNA once every 24 hours?
Recall that a human cell contains two copies of the human
genome, one inherited from the mother, the other from the
father, each consisting of 3 × 109 nucleotide pairs.
N
O
O–
O
dideoxycytosine
triphosphate (ddCTP)
H
H
NH2
N
O
–O
P
O
CH2
N
O
O–
E. None of the aberrant bases formed by deamination
occur naturally in DNA.
Question 6–8
CH2
O
B. Okazaki fragments are removed by a nuclease that
degrades RNA.
F. Cancer can result from the accumulation of mutations in
somatic cells.
H
NH2
A. A bacterial replication fork is asymmetrical because
it contains two DNA polymerase molecules that are
structurally distinct.
D. In the absence of DNA repair, genes are unstable.
O
N
O
O–
deoxycytosine
triphosphate (dCTP)
Which of the following statements are correct? Explain your
answers.
C. The error rate of DNA replication is reduced both by
proofreading by DNA polymerase and by DNA mismatch
repair.
CH2
O
O
dideoxycytosine
monophosphate (ddCMP)
H
H
Figure Q6–9
A. What would you expect if ddCTP were added to a DNA
replication reaction in large excess over the concentration of
the available deoxycytosine triphosphate (dCTP), the normal
deoxycytosine triphosphate?
B. What would happen if it were added at 10% of the
concentration of the available dCTP?
C. What effects would you expect if ddCMP were added
under the same conditions?
ECB4 EQ6.10/Q6.10
222
Chapter 6
DNA Replication, Repair, and Recombination
Question 6–10
Figure Q6–10 shows a snapshot of a replication fork in
which the RNA primer has just been added to the lagging
strand. Using this diagram as a guide, sketch the path of the
DNA as the next Okazaki fragment is synthesized. Indicate
the sliding clamp and the single-strand DNA-binding protein
as appropriate.
Question 6–15
Describe the consequences that would arise if a eukaryotic
chromosome
A. Contained only one origin of replication:
(i) at the exact center of the chromosome
(ii) at one end of the chromosome
B. Lacked one or both telomeres
C. Had no centromere
Assume that the chromosome is 150 million nucleotide pairs
in length, a typical size for an animal chromosome, and
that DNA replication in animal cells proceeds at about 100
nucleotides per second.
next primer
Question 6–16
Figure Q6–10
Question 6–11
Approximately how many high-energy bonds does DNA
polymerase use to replicate
a bacterial chromosome
ECB4 EQ6.12/Q6.12
(ignoring helicase and other enzymes associated with the
replication fork)? Compared with its own dry weight of
10–12 g, how much glucose does a single bacterium need to
provide enough energy to copy its DNA once? The number
of nucleotide pairs in the bacterial chromosome is 3 × 106.
Oxidation of one glucose molecule yields about 30 highenergy phosphate bonds. The molecular weight of glucose
is 180 g/mole. (Recall from Figure 2–3 that a mole consists
of 6 × 1023 molecules.)
Question 6–12
What, if anything, is wrong with the following statement:
“DNA stability in both reproductive cells and somatic cells is
essential for the survival of a species.” Explain your answer.
Question 6–13
NH2
O
H2O
A common type of chemical
H
C
C
damage to DNA is produced
N
N
by a spontaneous reaction
termed deamination, in which
NH3
a nucleotide base loses an
Figure Q6–13
amino group (NH2). The amino
group is replaced by a keto group (C=O), by the general
reaction shown in Figure Q6–13. Write the structures of the
bases A, G, C, T, and U and predict the products that will
be produced by deamination. By looking at the products of
this reaction—and remembering that, in the cell, these will
need to be recognized and repaired—can
youEQ6.15/Q6.15
propose an
ECB4
explanation for why DNA cannot contain uracil?
Question 6–14
A. Explain why telomeres and telomerase are needed
for replication of eukaryotic chromosomes but not for
replication of a circular bacterial chromosome. Draw a
diagram to illustrate your explanation.
B. Would you still need telomeres and telomerase to
complete eukaryotic chromosome replication if primase
always laid down the RNA primer at the very 3ʹ end of the
template for the lagging strand?
Because DNA polymerase proceeds only in the 5ʹ-to-3ʹ
direction, the enzyme is able to correct its own
polymerization errors as it moves along the DNA (Figure
Q6–16). A hypothetical DNA polymerase that synthesized
in the 3ʹ-to-5ʹ direction would be unable to proofread.
Given what you know about nucleic acid chemistry and DNA
synthesis, draw a sketch similar to Figure Q6–16 that shows
what would happen if a DNA polymerase operating in the
3ʹ-to-5ʹ direction were to remove an incorrect nucleotide
from a growing DNA strand. Why would the edited strand
be unable to be elongated?
CORRECT 5′-to-3′ STRAND GROWTH
5′
P
3′
P
P
end of growing
DNA strand
5′
HYDROLYSIS OF INCOMING
DEOXYRIBONUCLEOSIDE
TRIPHOSPHATE PROVIDES
ENERGY FOR
POLYMERIZATION
incorrect
deoxyribonucleoside
triphosphate
P Pi
5′
P
3′
P P P
3′
P
P
P
PROOFREADING
P
5′
P
3′
P
P
P P P
HYDROLYSIS OF INCOMING
DEOXYRIBONUCLEOTIDE
TRIPHOSPHATE PROVIDES
ENERGY FOR
POLYMERIZATION
correct
deoxyribonucleoside
triphosphate
P Pi
5′
P
Figure Q6–16
3′ end produced when
incorrect nucleotide
is removed by
proofreading
3′
P
P
P
HIGH-ENERGY BOND IS
CLEAVED, PROVIDING THE
ENERGY FOR POLYMERIZATION
chapter seven
7
From DNA to Protein:
How Cells Read the Genome
Once the double-helical structure of DNA (deoxyribonucleic acid) had
been determined in the early 1950s, it became clear that the hereditary
information in cells is encoded in the linear order—or sequence—of the
four different nucleotide subunits that make up the DNA. We saw in
Chapter 6 how this information can be passed on unchanged from a cell
to its descendants through the process of DNA replication. But how does
the cell decode and use the information? How do genetic instructions
written in an alphabet of just four “letters” direct the formation of a bacterium, a fruit fly, or a human? We still have a lot to learn about how the
information stored in an organism’s genes produces even the simplest
unicellular bacterium, let alone how it directs the development of complex multicellular organisms like ourselves. But the DNA code itself has
been deciphered, and we have come a long way in understanding how
cells read it.
Even before the DNA code was broken, it was known that the information
contained in genes somehow directed the synthesis of proteins. Proteins
are the principal constituents of cells and determine not only cell structure but also cell function. In previous chapters, we encountered some
of the thousands of different kinds of proteins that cells can make. We
saw in Chapter 4 that the properties and function of a protein molecule
are determined by the sequence of the 20 different amino acid subunits
in its polypeptide chain: each type of protein has its own unique amino
acid sequence, which dictates how the chain will fold to form a molecule
with a distinctive shape and chemistry. The genetic instructions carried
by DNA must therefore specify the amino acid sequences of proteins. We
will see in this chapter exactly how this is done.
from DNA to RNA
from RNA to protein
RNA and the origins of life
224
Chapter 7
From DNA to Protein: How Cells Read the Genome
gene
DNA
5′
3′
3′
5′
nucleotides
RNA SYNTHESIS
TRANSCRIPTION
RNA
3′
5′
PROTEIN SYNTHESIS
TRANSLATION
PROTEIN
COOH
H2N
amino acids
Figure 7–1 Genetic information directs
the synthesis of proteins. The flow of
genetic information from DNA to RNA
(transcription) and from RNA to protein
(translation) occurs in all living cells. It
was Francis Crick who dubbed this flow
of information “the central dogma.” The
segments of DNA that are transcribed into
RNA are called genes.
ECB4 E7.01/7.01
DNA does not synthesize proteins itself, but it acts like a manager, delegating the various tasks to a team of workers. When a particular protein
is needed by the cell, the nucleotide sequence of the appropriate segment
of a DNA molecule is first copied into another type of nucleic acid—RNA
(ribonucleic acid ). That segment of DNA is called a gene, and the resulting RNA copies are then used to direct the synthesis of the protein. Many
thousands of these conversions from DNA to protein occur every second in each cell in our body. The flow of genetic information in cells is
therefore from DNA to RNA to protein (Figure 7–1). All cells, from bacteria to humans, express their genetic information in this way—a principle
so fundamental that it has been termed the central dogma of molecular
biology.
In this chapter, we explain the mechanisms by which cells copy DNA
into RNA (a process called transcription) and then use the information
in RNA to make protein (a process called translation). We also discuss
a few of the key variations on this basic scheme. Principal among these
is RNA splicing, a process in eukaryotic cells in which segments of an
RNA transcript are removed—and the remaining segments stitched back
together—before the RNA is translated into protein. In the final section,
we consider how the present scheme of information storage, transcription, and translation might have arisen from much simpler systems in the
earliest stages of cell evolution.
From DNA to RNA
Transcription and translation are the means by which cells read out, or
express, the instructions in their genes. Many identical RNA copies can be
made from the same gene, and each RNA molecule can direct the synthesis of many identical protein molecules. This successive amplification
enables cells to rapidly synthesize large amounts of protein whenever
necessary. At the same time, each gene can be transcribed, and its RNA
translated, at different rates, providing the cell with a way to make vast
quantities of some proteins and tiny quantities of others (Figure 7–2).
Moreover, as we discuss in Chapter 8, a cell can change (or regulate) the
expression of each of its genes according to the needs of the moment.
In this section, we discuss the production of RNA, the first step in gene
expression.
Question 7–1
gene A
gene B
DNA
Consider the expression “central
dogma,” which refers to the flow
of genetic information from DNA
to RNA to protein. Is the word
“dogma” appropriate in this
context?
TRANSCRIPTION
TRANSCRIPTION
RNA
RNA
TRANSLATION
TRANSLATION
Figure 7–2 A cell can express different
genes at different rates. In this and later
figures, the untranscribed portions of the
DNA are shown in gray.
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
protein
B
B
B
protein
225
From DNA to RNA
(A)
HOCH2 O
OH
H
H
OH
H
OH
H
(B)
5′ end
SUGAR DIFFERENCES
HOCH2 O
H
–O
H
H
P
H
OH
ribose
deoxyribose
used in DNA
bases
O
O
HC
HC
U
N
O
H3C
NH
C
HC
C
O
C
T
N
–O
H
thymine
P
O
A
O
H2C
C
H
OH
O
NH
uracil
used in RNA
C
O
H 2C
BASE DIFFERENCES
C
O
O
H
used in RNA
sugar–phosphate
backbone
O
OH
O
O
–O
used in DNA
Figure 7–3 The chemical structure of RNA differs slightly from
that of DNA. (A) RNA contains the sugar ribose, which differs from
deoxyribose, the sugar used in DNA, by the presence of an additional
–OH group. (B) RNA contains the base uracil, which differs from
thymine, the equivalent base in DNA, by the absence of a –CH3 group.
(C) A short length of RNA. The chemical linkage between nucleotides
in RNA—a phosphodiester bond—is the same as that in DNA.
P
U
O
H2C
ribose
O
–O
OH
P
O
G
O
O
H 2C
O
OH
3′ end
(C)
3′
5′
H
H
C
Although their chemical differences are small, DNA and RNA differ quite
e7.03/7.03
dramatically in overall structure. Whereas DNA always occursECB4
in cells
as a double-stranded helix, RNA is single-stranded. This difference has
important functional consequences. Because an RNA chain is singlestranded, it can fold up into a variety of shapes, just as a polypeptide
chain folds up to form the final shape of a protein (Figure 7–5); doublestranded DNA cannot fold in this fashion. As we discuss later, the ability
to fold into a complex three-dimensional shape allows RNA to carry out
various functions in cells, in addition to conveying information between
DNA and protein. Whereas DNA functions solely as an information store,
some RNAs have structural, regulatory, or catalytic roles.
Figure 7–4 Uracil forms a base pair with adenine. The hydrogen
bonds that hold the base pair together are shown in red. Uracil has the
same base-pairing properties as thymine. Thus U-A base pairs in RNA
closely resemble T-A base pairs in DNA (see Figure 5–6A).
O
O
Portions of DNA Sequence Are Transcribed into RNA
The first step a cell takes in expressing one of its many thousands of
genes is to copy the nucleotide sequence of that gene into RNA. The process is called transcription because the information, though copied into
another chemical form, is still written in essentially the same language—
the language of nucleotides. Like DNA, RNA is a linear polymer made
of four different nucleotide subunits, linked together by phosphodiester
bonds. It differs from DNA chemically in two respects: (1) the nucleotides in RNA are ribonucleotides—that is, they contain the sugar ribose
(hence the name ribonucleic acid) rather than deoxyribose; (2) although,
like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains uracil (U) instead of the thymine (T) found in DNA
(Figure 7–3). Because U, like T, can base-pair by hydrogen-bonding with
A (Figure 7–4), the complementary base-pairing properties described for
DNA in Chapter 5 apply also to RNA.
OH
N
O
C
U
C
uracil
C
N
O
H
H
N
N
H
C
N
A
H
C
C
C
N
N
C
adenine
H
5′
3′
sugar–phosphate backbone
226
Chapter 7
From DNA to Protein: How Cells Read the Genome
G
U
A
U
G
C
C
A
G
U
U
A
G
C
C
G
C
A
U
A
C
G
U
C
CC U
G GG
A
G
C
U
U
A
A
A
U
C
G
A
A
U
U
U
A
U
G
C
A
U
U
A
C
G
U
A
U
A
C
AU
GC
AAA
UU
A
(A)
A
G
U
U
G
A
C
(C)
(B)
Figure 7–5 RNA molecules can form intramolecular base pairs and fold into specific structures. RNA is singlestranded, but it often contains short stretches of nucleotides that can base-pair with complementary sequences
found elsewhere on the same molecule. These interactions—along with some “nonconventional base-pair
interactions (e.g., A-G)—allow an RNA molecule to fold into a three-dimensional structure that is determined by its
sequence of nucleotides. (A) A diagram of a hypothetical, folded RNA structure showing only conventional (G-C and
A-U) base-pair interactions. (B) Incorporating nonconventional base-pair interactions (green) changes the structure of
the hypothetical RNA shown in (A). (C) Structure of an actual RNA molecule that is involved in RNA splicing. This RNA
contains a considerable amount of double-helical structure. The sugar–phosphate backbone is blue and the bases are
red; the conventional base-pair interactions are indicated by red “rungs” that are continuous, and nonconventional
base pairs are indicated by broken red rungs. For an additional view of RNA structure, see Movie 7.1.
ECB4 e7.05/7.05
Transcription Produces RNA That Is Complementary to
One Strand of DNA
5′
3′
coding strand
DNA
3′
5′
template strand
TRANSCRIPTION
5′
3′
RNA
Figure 7–6 Transcription of a gene
produces an RNA complementary to one
strand of DNA. The transcribed strand
of the gene, the bottom strand in this
example, is called the template strand.
The nontemplate strand of the gene
(here, shown at the top) is sometimes called
the coding strand
because
its sequence
ECB4
e7.06/7.06
is equivalent to the RNA product, as
shown. Which DNA strand serves as the
template varies, depending on the gene,
as we discuss later. By convention, an RNA
molecule is always depicted with its
5′ end—the first part to be synthesized—
to the left.
All the RNA in a cell is made by transcription, a process that has certain
similarities to DNA replication (discussed in Chapter 6). Transcription
begins with the opening and unwinding of a small portion of the DNA
double helix to expose the bases on each DNA strand. One of the two
strands of the DNA double helix then acts as a template for the synthesis of RNA. Ribonucleotides are added, one by one, to the growing RNA
chain; as in DNA replication, the nucleotide sequence of the RNA chain
is determined by complementary base-pairing with the DNA template.
When a good match is made, the incoming ribonucleotide is covalently
linked to the growing RNA chain by the enzyme RNA polymerase. The
RNA chain produced by transcription—the RNA transcript—is therefore
elongated one nucleotide at a time and has a nucleotide sequence exactly
complementary to the strand of DNA used as the template (Figure 7–6).
Transcription differs from DNA replication in several crucial respects.
Unlike a newly formed DNA strand, the RNA strand does not remain
hydrogen-bonded to the DNA template strand. Instead, just behind the
region where the ribonucleotides are being added, the RNA chain is displaced and the DNA helix re-forms. For this reason—and because only
one strand of the DNA molecule is transcribed—RNA molecules are
single-stranded. Further, because RNAs are copied from only a limited
region of DNA, RNA molecules are much shorter than DNA molecules;
DNA molecules in a human chromosome can be up to 250 million nucleotide pairs long, whereas most mature RNAs are no more than a few
thousand nucleotides long, and many are much shorter than that.
From DNA to RNA
RNA polymerase
5′
3′
3′
5′
DNA template
strand
5′
newly synthesized
RNA transcript
incoming
ribonucleoside
triphosphates
active site of
polymerase
ribonucleoside
triphosphate
tunnel
Like the DNA polymerase that carries out DNA replication (discussed
in Chapter 6), RNA polymerases catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the
sugar–phosphate backbone of the RNA chain (see Figure 7–3). The RNA
ECB4along
e7.07/7.07
polymerase moves stepwise
the DNA, unwinding the DNA helix
just ahead to expose a new region of the template strand for complementary base-pairing. In this way, the growing RNA chain is extended by
one nucleotide at a time in the 5′-to-3′ direction (Figure 7–7). The incoming ribonucleoside triphosphates (ATP, CTP, UTP, and GTP) provide the
energy needed to drive the reaction forward (see Figure 6–11).
The almost immediate release of the RNA strand from the DNA as it is synthesized means that many RNA copies can be made from the same gene
in a relatively short time; the synthesis of the next RNA is usually started
before the first RNA has been completed (Figure 7–8). A medium-sized
gene—say, 1500 nucleotide pairs—requires approximately 50 seconds for
a molecule of RNA polymerase to transcribe it (Movie 7.2). At any given
time, there could be dozens of polymerases speeding along this single
stretch of DNA, hard on one another’s heels, allowing more than 1000
transcripts to be synthesized in an hour. For most genes, however, the
amount of transcription is much less than this.
Although RNA polymerase catalyzes essentially the same chemical reaction as DNA polymerase, there are some important differences between
the two enzymes. First, and most obviously, RNA polymerase uses ribonucleoside for phosphates as substrates, so it catalyzes the linkage of
ribonucleotides, not deoxyribonucleotides. Second, unlike the DNA
polymerase involved in DNA replication, RNA polymerases can start an
RNA chain without a primer. This difference likely evolved because transcription need not be as accurate as DNA replication; unlike DNA, RNA is
not used as the permanent storage form of genetic information in cells,
so mistakes in RNA transcripts have relatively minor consequences for a
cell. RNA polymerases make about one mistake for every 104 nucleotides
copied into RNA, whereas DNA polymerase makes only one mistake for
every 107 nucleotides copied.
Cells Produce Various Types of RNA
The vast majority of genes carried in a cell’s DNA specify the amino acid
sequences of proteins. The RNA molecules encoded by these genes—which
1 μm
227
Figure 7–7 DNA is transcribed into RNA
by the enzyme RNA polymerase. RNA
polymerase (pale blue) moves stepwise
along the DNA, unwinding the DNA helix in
front of it. As it progresses, the polymerase
adds ribonucleotides one by one to the
RNA chain, using an exposed DNA strand as
a template. The resulting RNA transcript is
thus single-stranded and complementary to
this template strand (see Figure 7–6). As the
polymerase moves along the DNA template
(in the 3′-to-5′ direction), it displaces the
newly formed RNA, allowing the two strands
of DNA behind the polymerase to rewind.
A short region of hybrid DNA/RNA helix
(approximately nine nucleotides in length)
therefore forms only transiently, causing a
“window” of DNA/RNA helix to move along
the DNA with the polymerase (Movie 7.2).
Question 7–2
In the electron micrograph in Figure
7–8, are the RNA polymerase
molecules moving from right to left
or from left to right? Why are the
RNA transcripts so much shorter
than the DNA segments (genes) that
encode them?
Figure 7–8 Transcription can be visualized
in the electron microscope. The
micrograph shows many molecules of RNA
polymerase simultaneously transcribing two
adjacent ribosomal genes on a single DNA
molecule. Molecules of RNA polymerase
are barely visible as a series of tiny dots
along the spine of the DNA molecule;
each polymerase has an RNA transcript (a
short, fine thread) radiating from it. The
RNA molecules being transcribed from the
two ribosomal genes—ribosomal RNAs
(rRNAs)—are not translated into protein, but
are instead used directly as components of
ribosomes, macromolecular machines made
of RNA and protein. The large particles that
can be seen at the free, 5′ end of each rRNA
transcript are believed to be ribosomal
proteins that have assembled on the ends
of the growing transcripts. (Courtesy of
Ulrich Scheer.)
228
Chapter 7
From DNA to Protein: How Cells Read the Genome
ultimately direct the synthesis of proteins—are called messenger RNAs
(mRNAs). In eukaryotes, each mRNA typically carries information transcribed from just one gene, which codes for a single protein; in bacteria, a
set of adjacent genes is often transcribed as a single mRNA, which therefore carries the information for several different proteins.
The final product of other genes, however, is the RNA itself. As we see
later, these nonmessenger RNAs, like proteins, have various roles, serving as regulatory, structural, and catalytic components of cells. They play
key parts, for example, in translating the genetic message into protein:
ribosomal RNAs (rRNAs) form the structural and catalytic core of the ribosomes, which translate mRNAs into protein, and transfer RNAs (tRNAs) act
as adaptors that select specific amino acids and hold them in place on a
ribosome for their incorporation into protein. Other small RNAs, called
microRNAs (miRNAs), serve as key regulators of eukaryotic gene expression, as we discuss in Chapter 8. The most common types of RNA are
summarized in Table 7–1.
In the broadest sense, the term gene expression refers to the process
by which the information encoded in a DNA sequence is translated into
a product that has some effect on a cell or organism. In cases where
the final product of the gene is a protein, gene expression includes both
transcription and translation. When an RNA molecule is the gene’s final
product, however, gene expression does not require translation.
Signals in DNA Tell RNA Polymerase Where to Start and
Finish Transcription
The initiation of transcription is an especially critical process because it
is the main point at which the cell selects which proteins or RNAs are to
be produced. To begin transcription, RNA polymerase must be able to
recognize the start of a gene and bind firmly to the DNA at this site. The
way in which RNA polymerases recognize the transcription start site of a
gene differs somewhat between bacteria and eukaryotes. Because the
situation in bacteria is simpler, we describe it first.
When an RNA polymerase collides randomly with a DNA molecule, the
enzyme sticks weakly to the double helix and then slides rapidly along its
length. RNA polymerase latches on tightly only after it has encountered
a gene region called a promoter, which contains a specific sequence
of nucleotides that lies immediately upstream of the starting point for
RNA synthesis. Once bound tightly to this sequence, the RNA polymerase
opens up the double helix immediately in front of the promoter to expose
the nucleotides on each strand of a short stretch of DNA. One of the two
exposed DNA strands then acts as a template for complementary basepairing with incoming ribonucleoside triphosphates, two of which are
Table 7–1 Types of RNA Produced in Cells
Type of RNA
Function
messenger RNAs (mRNAs)
code for proteins
ribosomal RNAs (rRNAs)
form the core of the ribosome’s structure and
catalyze protein synthesis
microRNAs (miRNAs)
regulate gene expression
transfer RNAs (tRNAs)
serve as adaptors between mRNA and amino acids
during protein synthesis
other noncoding RNAs
used in RNA splicing, gene regulation, telomere
maintenance, and many other processes
From DNA to RNA
start
site
stop
site
gene
5′
3′
3′
5′
promoter
RNA polymerase
5′
3′
DNA
terminator
template strand
RNA SYNTHESIS
BEGINS
3′
5′
5′
SIGMA FACTOR RELEASED
POLYMERASE CLAMPS DOWN ON DNA;
RNA SYNTHESIS CONTINUES
5′
3′
3′
5′
5′
growing RNA transcript
TERMINATION AND RELEASE OF
BOTH POLYMERASE AND
COMPLETED RNA TRANSCRIPT
5′
3′
3′
5′
gene
3′
5′
SIGMA
FACTOR
REBINDS
joined together by the polymerase to begin synthesis of the RNA chain.
Chain elongation then continues until the enzyme encounters a second
signal in the DNA, the terminator (or stop site), where the polymerase
halts and releases both the DNA template and the newly made RNA transcript (Figure 7–9). This terminator sequence is contained within the
gene and is transcribed into the 3ʹ end of the newly made RNA.
ECB4 e7.09/7.09
Because the polymerase must bind tightly before transcription can begin,
a segment of DNA will be transcribed only if it is preceded by a promoter.
This ensures that those portions of a DNA molecule that contain a gene
will be transcribed into RNA. The nucleotide sequences of a typical promoter—and a typical terminator—are presented in Figure 7–10.
In bacteria, it is a subunit of RNA polymerase, the sigma (σ) factor (see
Figure 7–9), that is primarily responsible for recognizing the promoter
sequence on the DNA. But how can this factor “see” the promoter, given
that the base-pairs in question are situated in the interior of the DNA
double helix? It turns out that each base presents unique features to the
outside of the double helix, allowing the sigma factor to find the promoter
sequence without having to separate the entwined DNA strands.
The next problem an RNA polymerase faces is determining which of
the two DNA strands to use as a template for transcription: each strand
has a different nucleotide sequence and would produce a different RNA
transcript. The secret lies in the structure of the promoter itself. Every
promoter has a certain polarity: it contains two different nucleotide
sequences upstream of the transcriptional start site that position the RNA
polymerase, ensuring that it binds to the promoter in only one orientation
229
Figure 7–9 Signals in the nucleotide
sequence of a gene tell bacterial RNA
polymerase where to start and stop
transcription. Bacterial RNA polymerase
(light blue) contains a subunit called sigma
factor (yellow) that recognizes the promoter
of a gene (green). Once transcription has
begun, sigma factor is released, and the
polymerase moves forward and continues
synthesizing the RNA. Chain elongation
continues until the polymerase encounters a
sequence in the gene called the terminator
(red ). There the enzyme halts and releases
both the DNA template and the newly
made RNA transcript. The polymerase then
reassociates with a free sigma factor and
searches for another promoter to begin the
process again.
230
Chapter 7
From DNA to Protein: How Cells Read the Genome
Figure 7–10 Bacterial promoters
and terminators have specific
nucleotide sequences that are
recognized by RNA polymerase.
(A) The green-shaded regions
represent the nucleotide sequences
that specify a promoter. The
numbers above the DNA indicate
the positions of nucleotides
counting from the first nucleotide
transcribed, which is designated +1.
The polarity of the promoter orients
the polymerase and determines
which DNA strand is transcribed.
All bacterial promoters contain
DNA sequences at –10 and –35
that closely resemble those shown
here. (B) The red-shaded regions
represent sequences in the gene
that signal the RNA polymerase to
terminate transcription. Note that
the regions transcribed into RNA
contain the terminator but not the
promoter nucleotide sequences. By
convention, the sequence of a gene
is that of the non-template strand, as
this strand has the same sequence
as the transcribed RNA (with T
substituting for U).
(A)
_35
PROMOTER
5′
3′
_10
+1
TAGTGTATTGACATGATAGAAGCACTCTACTATATTCTCAATAGGTCCACG
ATCACATAACTGTACTATCTTCGTGAGATGATATAAGAGTTATCCAGGTGC
start
site
5′
(B)
3′
DNA
5′
template strand
TRANSCRIPTION
AGGUCCACG
3′
RNA
TERMINATOR
5′
3′
CCCACAGCCGCCAGTTCCGCTGGCGGCATTTTAACTTTCTTTAATGA
GGGTGTCGGCGGTCAAGGCGACCGCCGTAAAATTGAAAGAAATTACT
TRANSCRIPTION
template strand
5′
3′
5′
DNA
stop
site
CCCACAGCCGCCAGUUCCGCUGGCGGCAUUUU
3′
RNA
(see Figure 7–10A). Because the polymerase can only synthesize RNA
in the 5′-to-3′ direction once the enzyme is bound it must use the DNA
strand oriented in the 3′-to-5′ direction as its template.
This selection of a template strand does not mean that on a given chromosome, transcription always proceeds in the same direction. With
ECB4 e7.10/7.10
respect to the chromosome as a whole, the direction of transcription varies from gene to gene. But because each gene typically has only one
promoter, the orientation of its promoter determines in which direction
that gene is transcribed and therefore which strand is the template strand
(Figure 7–11).
Initiation of Eukaryotic Gene Transcription Is a Complex
Process
Many of the principles we just outlined for bacterial transcription also
apply to eukaryotes. However, transcription initiation in eukaryotes differs in several important ways from that in bacteria:
Figure 7–11 On an individual
chromosome, some genes are transcribed
using one DNA strand as a template,
and others are transcribed from the
other DNA strand. RNA polymerase
always moves in the 3′-to-5′ direction
and the selection of the template strand
is determined by the orientation of the
promoter (green arrowheads) at the
beginning of each gene. Thus the genes
transcribed from left to right use the bottom
DNA strand as the template (see Figure
7–10); those transcribed from right to left
use the top strand as the template.
•
The first difference lies in the RNA polymerases themselves. While
bacteria contain a single type of RNA polymerase, eukaryotic cells
have three—RNA polymerase I, RNA polymerase II, and RNA polymerase III. These polymerases are responsible for transcribing different
types of genes. RNA polymerases I and III transcribe the genes encoding transfer RNA, ribosomal RNA, and various other RNAs that play
structural and catalytic roles in the cell (Table 7–2). RNA polymerase
II transcribes the vast majority of eukaryotic genes, including all those
that encode proteins and miRNAs (Movie 7.3). Our subsequent discussion will therefore focus on RNA polymerase II.
•
A second difference is that, whereas the bacterial RNA polymerase
(along with its sigma subunit) is able to initiate transcription on its
own, eukaryotic RNA polymerases require the assistance of a large set
of accessory proteins. Principal among these are the general transcription factors, which must assemble at each promoter, along with the
polymerase, before the polymerase can begin transcription.
RNA transcript
from gene b
promoter
5′
3′
gene a
gene b
RNA transcript
from gene a
ECB4 e7.11/7.11
3′
DNA
5′
promoter
From DNA to RNA
Table 7–2 The Three RNA Polymerases in Eukaryotic Cells
•
•
Type of Polymerase
Genes Transcribed
RNA polymerase I
most rRNA genes
RNA polymerase II
all protein-coding genes, miRNA genes, plus
genes for other noncoding RNAs (e.g., those in
spliceosomes)
RNA polymerase III
tRNA genes
5S rRNA gene
genes for many other small RNAs
A third distinctive feature of transcription in eukaryotes is that the
mechanisms that control its initiation are much more elaborate than
those in prokaryotes—a point we discuss in detail in Chapter 8. In bacteria, genes tend to lie very close to one another in the DNA, with only
very short lengths of nontranscribed DNA between them. But in plants
and animals, including humans, individual genes are spread out along
the DNA, with stretches of up to 100,000 nucleotide pairs between one
gene and the next. This architecture allows a single gene to be controlled by a large variety of regulatory DNA sequences scattered along
the DNA, and it enables eukaryotes to engage in more complex forms
of transcriptional regulation than do bacteria.
Last but not least, eukaryotic transcription initiation must take into
account the packing of DNA into nucleosomes and more compact
forms of chromatin structure, as we describe in Chapter 8.
We now turn to the general transcription factors and discuss how they
help eukaryotic RNA polymerase II initiate transcription.
Question 7–3
Could the RNA polymerase used
for transcription be used as the
polymerase that makes the RNA
primer required for DNA replication
(discussed in Chapter 6)?
start of transcription
TATA box
DNA
(A)
TBP
(B)
Eukaryotic RNA Polymerase Requires General
Transcription Factors
The initial finding that, unlike bacterial RNA polymerase, purified eukaryotic RNA polymerase II could not initiate transcription on its own in a
test tube led to the discovery and purification of the general transcription factors. These accessory proteins assemble on the promoter, where
they position the RNA polymerase and pull apart the DNA double helix
to expose the template strand, allowing the polymerase to begin transcription. Thus the general transcription factors have a similar role in
eukaryotic transcription as sigma factor has in bacterial transcription.
TFIID
TFIIB
(C)
TFIIF
other factors
TFIIE
TFIIH
RNA polymerase II
Figure 7–12 shows how the general transcription factors assemble at
a promoter used by RNA polymerase II. The assembly process typically
begins with the binding of the general transcription factor TFIID to a short
Figure 7–12 To begin transcription, eukaryotic RNA polymerase II
requires a set of general transcription factors. These transcription
factors are called TFIIB, TFIID, and so on. (A) Many eukaryotic
promoters contain a DNA sequence called the TATA box. (B) The
TATA box is recognized by a subunit of the general transcription factor
TFIID, called the TATA-binding protein (TBP). For simplicity, the DNA
distortion produced by the binding of the TBP (see Figure 7–13) is
not shown. (C) The binding of TFIID enables the adjacent binding of
TFIIB. (D) The rest of the general transcription factors, as well as the
RNA polymerase itself, assemble at the promoter. (E) TFIIH then pries
apart the double helix at the transcription start point, using the energy
of ATP hydrolysis, which exposes the template strand of the gene (not
shown). TFIIH also phosphorylates RNA polymerase II, releasing the
polymerase from most of the general transcription factors, so it can
begin transcription. The site of phosphorylation is a long polypeptide
“tail” that extends from the polymerase.
(D)
ribonucleoside
triphosphates
(UTP, ATP, CTP, GTP)
(E)
P
P
RNA
TRANSCRIPTION
231
232
Chapter 7
From DNA to Protein: How Cells Read the Genome
N
A
G
A
A
C
A
T
A
Figure 7–13 TATA-binding protein (TBP) binds to the TATA box
(indicated by letters) and bends the DNA double helix. The unique
distortion of DNA caused by TBP, which is a subunit of TFIID (see
Figure 7–12), helps attract the other general transcription factors.
TBP is a single polypeptide chain that is folded into two very similar
domains (blue and green). The protein sits atop the DNA double helix
like a saddle on a bucking horse (Movie 7.4). (Adapted from J.L. Kim
et al., Nature 365:520–527, 1993. With permission from Macmillan
Publishers Ltd.)
T
5′
5′
3′
3′
ECB4 e7.13/7.13
nuclear
envelope
segment of DNA double helix composed primarily of T and A nucleotides;
because of its composition, this part of the promoter is known as the TATA
box. Upon binding to DNA, TFIID causes a dramatic local distortion in the
DNA double helix (Figure 7–13), which helps to serve as a landmark for
the subsequent assembly of other proteins at the promoter. The TATA box
is a key component of many promoters used by RNA polymerase II, and
it is typically located 25 nucleotides upstream from the transcription start
site. Once TFIID has bound to the TATA box, the other factors assemble,
along with RNA polymerase II, to form a complete transcription initiation
complex. Although Figure 7–12 shows the general transcription factors
piling onto the promoter in a certain order, the actual order of assembly
probably differs from one promoter to the next.
After RNA polymerase II has been positioned on the promoter, it must be
released from the complex of general transcription factors to begin its task
of making an RNA molecule. A key step in liberating the RNA polymerase is the addition of phosphate groups to its “tail” (see Figure 7–12E).
This liberation is initiated by the general transcription factor TFIIH, which
contains a protein kinase as one of its subunits. Once transcription has
begun, most of the general transcription factors dissociate from the DNA
and then are available to initiate another round of transcription with a
new RNA polymerase molecule. When RNA polymerase II finishes transcribing a gene, it too is released from the DNA; the phosphates on its
tail are stripped off by protein phosphatases, and the polymerase is then
ready to find a new promoter. Only the dephosphorylated form of RNA
polymerase II can initiate RNA synthesis.
nucleolus
Eukaryotic mRNAs Are Processed in the Nucleus
Although the templating principle by which DNA is transcribed into RNA
is the same in all organisms, the way in which the RNA transcripts are
handled before they can be used by the cell to make protein differs greatly
between bacteria and eukaryotes. Bacterial DNA lies directly exposed
to the cytoplasm, which contains the ribosomes on which protein synthesis takes place. As an mRNA molecule in a bacterium starts to be
synthesized, ribosomes immediately attach to the free 5′ end of the RNA
transcript and begin translating it into protein.
cytosol
nucleus
5 μm
Figure 7–14 Before they can be
translated, mRNA molecules made in
the nucleus must be exported to the
cytosol via pores in the nuclear envelope
(red arrows). Shown here is a section of a
liver cell nucleus. The nucleolus is where
ribosomal RNAs are synthesized and
combined with proteins to form ribosomes,
ECB4 e7.14/7.14
which are then exported to the cytoplasm.
(From D.W. Fawcett, A Textbook of
Histology, 11th ed. Philadelphia: Saunders,
1986. With permission from Elsevier.)
In eukaryotic cells, by contrast, DNA is enclosed within the nucleus.
Transcription takes place in the nucleus, but protein synthesis takes
place on ribosomes in the cytoplasm. So, before a eukaryotic mRNA
can be translated into protein, it must be transported out of the nucleus
through small pores in the nuclear envelope (Figure 7–14). Before it can
be exported to the cytosol, however, a eukaryotic RNA must go through
several RNA processing steps, which include capping, splicing, and polyadenylation, as we discuss shortly. These steps take place as the RNA is
being synthesized. The enzymes responsible for RNA processing ride on
the phosphorylated tail of eukaryotic RNA polymerase II as it synthesizes
an RNA molecule (see Figure 7–12), and they process the transcript as it
emerges from the polymerase (Figure 7–15).
From DNA to RNA
Different types of RNA are processed in different ways before leaving the
nucleus. Two processing steps, capping and polyadenylation, occur only
on RNA transcripts destined to become mRNA molecules (called precursor mRNAs, or pre-mRNAs).
233
RNA polymerase II
DNA
P P
1. RNA capping modifies the 5′ end of the RNA transcript, the end that
is synthesized first. The RNA is capped by the addition of an atypical
nucleotide—a guanine (G) nucleotide bearing a methyl group, which
is attached to the 5′ end of the RNA in an unusual way (Figure 7–16).
This capping occurs after RNA polymerase II has produced about 25
nucleotides of RNA, long before it has completed transcribing the
whole gene.
P
P
splicing
factors
polyadenylation
factors
capping factors
P P
2. Polyadenylation provides a newly transcribed mRNA with a special structure at its 3′ end. In contrast with bacteria, where the 3′ end
of an mRNA is simply the end of the chain synthesized by the RNA
polymerase, the 3′ end of a forming eukaryotic mRNA is first trimmed
by an enzyme that cuts the RNA chain at a particular sequence of
nucleotides. The transcript is then finished off by a second enzyme
that adds a series of repeated adenine (A) nucleotides to the cut end.
This poly-A tail is generally a few hundred nucleotides long (see Figure
7–16A).
P
P
mRNA
RNA
PROCESSING
BEGINS
Figure 7–15 Phosphorylation of the tail of
RNA polymerase II allows RNA-processing
proteins to assemble there. Note that the
phosphates shown here are in addition to
the ones required for transcription initiation
(see FigureECB4
7–12).
Capping, polyadenylation,
e7.15/7.15
and splicing are all modifications that occur
during RNA processing in the nucleus.
These two modifications—capping and polyadenylation—increase the
stability of a eukaryotic mRNA molecule, facilitate its export from the
nucleus to the cytoplasm, and generally mark the RNA molecule as an
mRNA. They are also used by the protein-synthesis machinery to make
sure that both ends of the mRNA are present and that the message is
therefore complete before protein synthesis begins.
In Eukaryotes, Protein-Coding Genes Are Interrupted by
Noncoding Sequences Called Introns
Most eukaryotic pre-mRNAs have to undergo an additional processing
step before they are functional mRNAs. This step involves a far more
radical modification of the pre-mRNA transcript than capping or polyadenylation, and it is the consequence of a surprising feature of most
eukaryotic genes. In bacteria, most proteins are encoded by an uninterrupted stretch of DNA sequence that is transcribed into an mRNA that,
without any further processing, can be translated into protein. Most protein-coding eukaryotic genes, in contrast, have their coding sequences
interrupted by long, noncoding, intervening sequences called introns.
The scattered pieces of coding sequence—called expressed sequences or
HO OH
CH2 P
5′
N+
Figure 7–16 Eukaryotic pre-mRNA molecules are modified by
capping and polyadenylation. (A) A eukaryotic mRNA has a cap
at the 5′ end and a poly-A tail at the 3′ end. Note that not all of the
RNA transcript shown codes for protein. (B) The structure of the
5′ cap. Many eukaryotic mRNA caps carry an additional modification:
the 2′-hydroxyl group on the second ribose sugar in the mRNA is
methylated (not shown).
5′ end of initial
RNA transcript
5′ cap
CH3
P
P
5′
CH2
5′-to-5′
triphosphate
bridge
OH
P
7-methylguanosine
CH2
OH
RNA capping and polyadenylation
+ 5′
G
P
coding
sequence
P P P
CH3
RNA
noncoding
sequence
AAAAA150–250
CH2
3′
poly-A tail
5′ cap
(A)
OH
protein
(B)
234
Chapter 7
From DNA to Protein: How Cells Read the Genome
coding region
5′
3′
3′
5′
DNA
bacterial gene
coding regions
(exons)
noncoding regions
(introns)
3′
5′
5′
3′
DNA
eukaryotic gene
Figure 7–17 Eukaryotic and bacterial genes are organized differently. A bacterial
gene consists of a single stretch of uninterrupted nucleotide sequence that encodes
the amino acid sequence of a protein (or more than one protein). In contrast, the
protein-coding sequences of most eukaryotic genes (exons) are interrupted by
noncoding sequences (introns). Promoters for transcription are indicated in green.
E7.17/7.17
exons—are usually ECB4
shorter
than the introns, and they often represent
only a small fraction of the total length of the gene (Figure 7–17). Introns
range in length from a single nucleotide to more than 10,000 nucleotides.
Some protein-coding eukaryotic genes lack introns altogether, and some
have only a few; but most have many (Figure 7–18). Note that the terms
“exon” and “intron” apply to both the DNA and the corresponding RNA
sequences.
Introns Are Removed From Pre-mRNAs by RNA Splicing
To produce an mRNA in a eukaryotic cell, the entire length of the gene,
introns as well as exons, is transcribed into RNA. After capping, and as
RNA polymerase II continues to transcribe the gene, the process of RNA
splicing begins, in which the introns are removed from the newly synthesized RNA and the exons are stitched together. Each transcript ultimately
receives a poly-A tail; in some cases, this happens after splicing, whereas
in other cases, it occurs before the final splicing reactions have been
completed. Once a transcript has been spliced and its 5′ and 3′ ends have
been modified, the RNA is now a functional mRNA molecule that can
leave the nucleus and be translated into protein.
Figure 7–18 Most proteincoding human genes are
broken into multiple exons
and introns. (A) The β-globin
gene, which encodes one of
the subunits of the oxygencarrying protein hemoglobin,
contains 3 exons. (B) The
Factor VIII gene, which
encodes a protein (Factor VIII)
that functions in the bloodclotting pathway, contains 26
exons. Mutations in this large
gene are responsible for the
most prevalent form of the
blood disorder hemophilia.
How does the cell determine which parts of the RNA transcript to remove
during splicing? Unlike the coding sequence of an exon, most of the
nucleotide sequence of an intron is unimportant. Although there is little overall resemblance between the nucleotide sequences of different
introns, each intron contains a few short nucleotide sequences that act
as cues for its removal from the pre-mRNA. These special sequences are
found at or near each end of the intron and are the same or very similar in
all introns (Figure 7–19). Guided by these sequences, an elaborate splicing machine cuts out the intron in the form of a “lariat” structure (Figure
7–20), formed by the reaction of the “A” nucleotide highlighted in red in
Figures 7–19 and 7–20.
human β-globin gene
human Factor VIII gene
123
1
5
introns
10
14
DNA
exons
(A)
2000
nucleotide pairs
(B)
200,000 nucleotide pairs
22
25
26
From DNA to RNA
235
sequences required for intron removal
5′
– – – AG GURAGU – –
exon 1
3′
– – YURAC – .... – YYYYYYYYNCAG G – – –
intron
portion of
pre-mRNA
exon 2
INTRON REMOVED
5′
3′
portion of
– – – AG G – – –
spliced mRNA
exon 1
exon 2
Figure 7–19 Special nucleotide sequences in a pre-mRNA transcript signal the
beginning and the end of an intron. Only the nucleotide sequences shown are
required to remove an intron; the other positions in an intron can be occupied by
any nucleotide. The special sequences are recognized primarily by small nuclear
ribonucleoproteins (snRNPs), which direct the cleavage of the RNA at the intron–
exon borders and catalyze the covalent linkage of the exon sequences. Here, in
addition to the standard symbols for nucleotides (A, C, G, U), R stands for either A
or G; Y stands for either C or U; N stands for any nucleotide. The A shown in red
forms the branch point of the lariat produced in the splicing reaction shown in Figure
7–20. The distances along the RNA between the three splicing sequences are highly
variable; however, the distance between the branch point and the 5′ splice junction is
typically much longer than that between the 3′ splice junction and the branch point
(see Figure 7–20). The splicing sequences shown are from humans; similar sequences
direct RNA splicing in other eukaryotes.
ECB4 e7.19/7.19
We will not describe the splicing machinery in detail, but it is worthwhile
to note that, unlike the other steps of mRNA production we have discussed, RNA splicing is carried out largely by RNA molecules rather than
proteins. These RNA molecules, called small nuclear RNAs (snRNAs),
are packaged with additional proteins to form small nuclear ribonucleoproteins (snRNPs, pronounced “snurps”). The snRNPs recognize splice-site
sequences through complementary base-pairing between their RNA
components and the sequences in the pre-mRNA, and they also participate intimately in the chemistry of splicing (Figure 7–21). Together, these
snRNPs form the core of the spliceosome, the large assembly of RNA and
protein molecules that carries out RNA splicing in the nucleus. To watch
the spliceosome in action, see Movie 7.5.
The intron–exon type of gene arrangement in eukaryotes may, at first,
seem wasteful. It does, however, have a number of important benefits.
First, the transcripts of many eukaryotic genes can be spliced in different ways, each of which can produce a distinct protein. Such alternative
splicing thereby allows many different proteins to be produced from
the same gene (Figure 7–22). About 95% of human genes are thought to
undergo alternative splicing. Thus RNA splicing enables eukaryotes to
increase the already enormous coding potential of their genomes.
RNA splicing also provides another advantage to eukaryotes, one that is
likely to have been profoundly important in the early evolutionary history
of genes. As we discuss in detail in Chapter 9, the intron–exon structure
of genes is thought to have sped up the emergence of new and useful
proteins: novel proteins appear to have arisen by the mixing and matching of different exons of preexisting genes, much like the assembly of a
new type of machine from a kit of preexisting functional components.
Indeed, many proteins in present-day cells resemble patchworks composed from a common set of protein pieces, called protein domains (see
Figure 4–51).
intron sequence
2′ HO A
5′
exon 1
OH
portion of
3′
pre-mRNA
exon 2
A
5′
3′
lariat
A
+
5′
3′
OH
portion of spliced
3′ pre-mRNA
Figure 7–20 An intron in a pre-mRNA
molecule forms a branched structure
during RNA splicing. In the first step, the
branch point adenine (red A) in the intron
sequence attacks the 5′ splice site and cuts
the sugar–phosphate backbone of the RNA
at this point (this is the same A highlighted
e7.20/7.20
in red ECB4
in Figure
7–19). In this process, the
cut 5′ end of the intron becomes covalently
linked to the 2′-OH group of the ribose
of the A nucleotide to form a branched
structure. The free 3′-OH end of the exon
sequence then reacts with the start of
the next exon sequence, joining the two
exons together into a continuous coding
sequence and releasing the intron in the
form of a lariat structure, which is eventually
degraded in the nucleus.
236
Chapter 7
From DNA to Protein: How Cells Read the Genome
Figure 7–21 Splicing is carried out by
a collection of RNA–protein complexes
called snRNPs. There are five snRNPs,
called U1, U2, U4, U5, and U6. As shown
here, U1 and U2 bind to the 5′ splice site
(U1) and the lariat branch point (U2) through
complementary base-pairing. Additional
snRNPs are attracted to the splice site,
and interactions between their protein
components drive the assembly of the
complete spliceosome. Rearrangements
in the base pairs that hold together the
snRNPs and the RNA transcript then
reorganize the spliceosome to form the
active site that excises the intron,
leaving the spliced mRNA behind
(see also Figure 7–20).
RNA portion of snRNP base-pairs
with sequences that signal
splicing
U1
U2
5′
3′
A
exon 1
portion of
pre-mRNA
exon 2
BINDING OF ADDITIONAL snRNPs;
ASSEMBLY OF SPLICEOSOME
U4/U6
U1
U2
5′
3′
A
U5
excised intron in
form of a lariat
SPLICING
U1
U2
A
5′
exon 1
exon 2
3′
portion of spliced mRNA
Mature Eukaryotic mRNAs Are Exported from the Nucleus
We have seen how eukaryotic pre-mRNA synthesis and processing take
ECB4
n7.100/7.21
place in an orderly fashion
within
the cell nucleus. However, these events
create a special problem for eukaryotic cells: of the total number of premRNA transcripts that are synthesized, only a small fraction—the mature
mRNAs—will be useful to the cell. The remaining RNA fragments—
excised introns, broken RNAs, and aberrantly spliced transcripts—are not
only useless, but they could be dangerous to the cell if allowed to leave
the nucleus. How, then, does the cell distinguish between the relatively
rare mature mRNA molecules it needs to export to the cytosol and the
overwhelming amount of debris generated by RNA processing?
The answer is that the transport of mRNA from the nucleus to the
cytosol, where mRNAs are translated into protein, is highly selective:
only correctly processed mRNAs are exported. This selective transport
is mediated by nuclear pore complexes, which connect the nucleoplasm
with the cytosol and act as gates that control which macromolecules can
enter or leave the nucleus (discussed in Chapter 15). To be “export ready,”
an mRNA molecule must be bound to an appropriate set of proteins, each
of which recognizes different parts of a mature mRNA molecule. These
proteins include poly-A–binding proteins, a cap-binding complex, and
exon 1
5′
3′
exon 2
exon 3
3′
5′
DNA
TRANSCRIPTION
Figure 7–22 Some pre-mRNAs undergo
alternative RNA splicing to produce
various mRNAs and proteins from the
same gene. Whereas all exons are present
in a pre-mRNA, some exons can be
excluded from the final mRNA molecule. In
this example, three of four possible mRNAs
are produced. The 5′ caps and poly-A tails
on the mRNAs are not shown.
exon 1
5′
exon 2
exon 3
ALTERNATIVE PRE-mRNA
SPLICING
1
2
3
2
3
three alternative mRNAs
1
2
3′ pre-mRNA
From DNA to RNA
237
nuclear
envelope
exon
junction
complex
5′ cap
nuclear pore
complex
AAAA
cap-binding
protein
AA
initiation factors
for protein synthesis
AAAAAA
PROTEIN
EXCHANGE
poly-A–binding
protein
NUCLEUS
TRANSLATION
AAAAAAA
CYTOSOL
proteins that bind to mRNAs that have been appropriately spliced (Figure
7–23). The entire set of bound proteins, rather than any single protein,
ultimately determines whether an mRNA molecule will leave the nucleus.
The “waste RNAs” that remain behind in the nucleus are degraded there,
and their nucleotide building blocks are reused for transcription.
ECB4 e7.22/7.23
mRNA Molecules Are Eventually Degraded in the Cytosol
Because a single mRNA molecule can be translated into protein many
times (see Figure 7–2), the length of time that a mature mRNA molecule persists in the cell affects the amount of protein it produces. Each
mRNA molecule is eventually degraded into nucleotides by ribonucleases
(RNAses) present in the cytosol, but the lifetimes of mRNA molecules differ considerably—depending on the nucleotide sequence of the mRNA
and the type of cell. In bacteria, most mRNAs are degraded rapidly, having a typical lifetime of about 3 minutes. The mRNAs in eukaryotic cells
usually persist longer: some, such as those encoding β-globin, have lifetimes of more than 10 hours, whereas others have lifetimes of less than
30 minutes.
These different lifetimes are in part controlled by nucleotide sequences
in the mRNA itself, most often in the portion of RNA called the 3′ untranslated region, which lies between the 3′ end of the coding sequence and
the poly-A tail. The different lifetimes of mRNAs help the cell control the
amount of each protein that it synthesizes. In general, proteins made in
large amounts, such as β-globin, are translated from mRNAs that have
long lifetimes, whereas proteins made in smaller amounts, or whose levels must change rapidly in response to signals, are typically synthesized
from short-lived mRNAs.
The Earliest Cells May Have Had Introns in Their Genes
The process of transcription is universal: all cells use RNA polymerase
and complementary base-pairing to synthesize RNA from DNA. Indeed,
bacterial and eukaryotic RNA polymerases are almost identical in overall
structure and clearly evolved from a shared ancestral polymerase. It may
therefore seem puzzling that the resulting RNA transcripts are handled so
differently in eukaryotes and in prokaryotes (Figure 7–24). In particular,
RNA splicing seems to mark a fundamental difference between those two
types of cells. But how did this dramatic difference arise?
As we have seen, RNA splicing provides eukaryotes with the ability to
produce a variety of proteins from a single gene. It also allows them
to evolve new genes by mixing-and-matching exons from preexisting
genes, as we discuss in Chapter 9. However, these advantages come with
a cost: the cell has to maintain a larger genome and has to discard a
Figure 7–23 A specialized set of RNAbinding proteins signals that a mature
mRNA is ready for export to the cytosol.
As indicated on the left, the cap and
poly-A tail of a mature mRNA molecule
are “marked” by proteins that recognize
these modifications. In addition, a group of
proteins called the exon junction complex
is deposited on the pre-mRNA after each
successful splice has occurred. Once the
mRNA is deemed “export ready,” a nuclear
transport receptor (discussed in Chapter
15) associates with the mRNA and guides it
through the nuclear pore. In the cytosol, the
mRNA can shed some of these proteins and
bind new ones, which, along with poly-A–
binding protein, act as initiation factors for
protein synthesis, as we discuss later.
238
(A)
Chapter 7
From DNA to Protein: How Cells Read the Genome
EUKARYOTES
(B)
PROKARYOTES
DNA
CYTOPLASM
TRANSCRIPTION
NUCLEUS
introns
mRNA
exons
DNA
TRANSLATION
protein
TRANSCRIPTION
pre-mRNA
RNA cap
5′ CAPPING
RNA SPLICING
3′ POLYADENYLATION
AAAA
mRNA
EXPORT
AAAA
mRNA
TRANSLATION
protein
Figure 7–24 Prokaryotes and eukaryotes
handle their RNA transcripts differently.
(A) In eukaryotic cells, the pre-mRNA
molecule produced by transcription
contains both intron and exon sequences.
Its two ends are modified, and the introns
are removed by RNA splicing. The resulting
mRNA is then transported from the nucleus
to the cytoplasm, where it is translated into
protein. Although these steps are depicted
as occurring in sequence, one at a time,
in reality they occur simultaneously. For
example, the RNA cap is usually added and
splicing usually begins before transcription
has been completed. Because of this
overlap, transcripts of the entire gene
(including all introns and exons) do not
typically exist in the cell. (B) In prokaryotes,
the production of mRNA molecules
is simpler. The 5′ end of an mRNA
molecule is produced by the initiation of
transcription by RNA polymerase, and the
3′ end is produced by the termination of
transcription. Because prokaryotic cells
lack a nucleus, transcription and translation
take place in a common compartment.
Translation of a bacterial mRNA can
therefore begin before its synthesis has
been completed. In both eukaryotes and
prokaryotes, the amount of a protein in a
cell depends on the rates of each of these
steps, as well as on the rates of degradation
of the mRNA and protein molecules.
large fraction of the RNA it synthesizes without ever using it. According
to one school of thought, early cells—the common ancestors of prokaryotes and eukaryotes—contained introns that were lost in prokaryotes
during subsequent evolution. By shedding their introns and adopting a
smaller, more streamlined genome, prokaryotes would have been able to
reproduce more rapidly and efficiently. Consistent with this idea, simple
eukaryotes that reproduce rapidly (some yeasts, for example) have relatively few introns, and these introns are usually much shorter than those
e7.23/7.24
foundECB4
in higher
eukaryotes.
On the other hand, some argue that introns were originally parasitic
mobile genetic elements (discussed in Chapter 9) that happened to
invade an early eukaryotic ancestor, colonizing its genome. These host
cells then unwittingly replicated the “stowaway” nucleotide sequences
along with their own DNA; modern eukaryotes simply never bothered
to sweep away the genetic clutter left from that ancient infection. The
issue, however, is far from settled; whether introns evolved early—and
were lost in prokaryotes—or evolved later in eukaryotes is still a topic of
scientific debate, and we return to it in Chapter 9.
From RNA to Protein
By the end of the 1950s, biologists had demonstrated that the information encoded in DNA is copied first into RNA and then into protein. The
debate then shifted to the “coding problem”: How is the information in
a linear sequence of nucleotides in an RNA molecule translated into the
linear sequence of a chemically quite different set of subunits—the amino
acids in a protein? This fascinating question intrigued scientists at the
time. Here was a cryptogram set up by nature that, after more than 3
billion years of evolution, could finally be solved by one of the products
of evolution—human beings! Indeed, scientists have not only cracked
the code but have revealed, in atomic detail, the precise workings of the
machinery by which cells read this code.
239
From RNA to Protein
codons
amino
acids
GCA
GCC
GCG
GCU
AGA
UUA
AGC
AGG
UUG
AGU
GGA
CUA
CGA
CCA UCA ACA
GUA
AUA CUC
GGC
CGC
CCC UCC ACC
GUC
AUC
UUC CCG UCG ACG
CGG GAC AAC UGC GAA CAA GGG CAC
CUG AAA
UAC GUG
AUU
CGU GAU AAU UGU GAG CAG GGU CAU
CUU AAG AUG UUU CCU UCU ACU UGG UAU GUU
Ala
Arg
A
R
Asp
D
Asn
N
Cys
C
Glu
E
Gln
Q
Gly
G
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
H
I
L
K
M
F
P
S
T
W
Y
V
UAA
UAG
UGA
stop
Figure 7–25 The nucleotide sequence of an mRNA is translated into the amino acid sequence of a protein via the genetic code.
All the three-nucleotide codons in mRNAs that specify a given amino acid are listed above that amino acid, which is given in both its
three-letter and one-letter abbreviations (see Panel 2–5, pp. 74–75, for the full name of each amino acid and its structure). Like RNA
molecules, codons are always written with the 5′-terminal nucleotide to the left. Note that most amino acids are represented by more
than one codon, and there are some regularities in the set of codons that specify each amino acid. Codons for the same amino acid tend
to contain the same nucleotides at the first and second positions and to vary at the third position. There are three codons that do not
specify any amino acid but act as termination sites (stop codons), signaling the end of the protein-coding sequence in an mRNA. One
codon—AUG—acts both as an initiation codon, signaling the start of a protein-coding message, and as the codon that specifies the
ECB4 e7.24/7.25
amino acid methionine.
An mRNA Sequence Is Decoded in Sets of Three
Nucleotides
Transcription as a means of information transfer is simple to understand:
DNA and RNA are chemically and structurally similar, and DNA can act as
a direct template for the synthesis of RNA through complementary basepairing. As the term transcription signifies, it is as if a message written
out by hand were being converted, say, into a typewritten text. The language itself and the form of the message do not change, and the symbols
used are closely related.
In contrast, the conversion of the information in RNA into protein represents a translation of the information into another language that
uses different symbols. Because there are only 4 different nucleotides in
mRNA but 20 different types of amino acids in a protein, this translation
cannot be accounted for by a direct one-to-one correspondence between
a nucleotide in RNA and an amino acid in protein. The rules by which the
nucleotide sequence of a gene, through an intermediary mRNA molecule,
is translated into the amino acid sequence of a protein are known as the
genetic code.
In 1961, it was discovered that the sequence of nucleotides in an mRNA
molecule is read consecutively in groups of three. And because RNA is
made of 4 different nucleotides, there are 4 × 4 × 4 = 64 possible combinations of three nucleotides: AAA, AUA, AUG, and so on. However, only
20 different amino acids are commonly found in proteins. Either some
nucleotide triplets are never used, or the code is redundant, with some
amino acids being specified by more than one triplet. The second possibility turned out to be correct, as shown by the completely deciphered
genetic code shown in Figure 7–25. Each group of three consecutive
nucleotides in RNA is called a codon, and each codon specifies one
amino acid. The strategy by which this code was cracked is described in
How We Know, pp. 240–241.
The same genetic code is used in nearly all present-day organisms.
Although a few slight differences have been found, these occur chiefly in
the mRNA of mitochondria and of some fungi and protozoa. Mitochondria
have their own DNA replication, transcription, and protein-synthesis machinery, which operates independently from the corresponding
machinery in the rest of the cell (discussed in Chapter 14), and they have
been able to accommodate minor changes to the otherwise universal
genetic code. Even in fungi and protozoa, the similarities in the code far
outweigh the differences.
In principle, an mRNA sequence can be translated in any one of three different reading frames, depending on where the decoding process begins
(Figure 7–26). However, only one of the three possible reading frames
1
5′
CUC
Leu
2
3
C
CU
AGC
GUU
ACC
Ser
Val
Thr
3′
AU
UCA
GCG
UUA
CCA
Ser
Ala
Leu
Pro
CAG
CGU
UAC
Gln
Arg
Tyr
U
CAU
His
Figure 7–26 In principle, an mRNA
molecule can be translated in three
possible reading frames. In the process of
translating a nucleotide sequence (blue) into
an amino acid sequence (red), the sequence
of nucleotides in an mRNA molecule is read
from the 5′ to the 3′ end in sequential sets
of three nucleotides. In principle, therefore,
the same mRNA sequence can specify three
completely different amino acid sequences,
depending on where translation begins—
that is, on the reading frame used. In reality,
however, only one of these reading frames
encodes the actual message and is therefore
used in translation, as we discuss later.
ECB4 e7.25/7.26
240
How we Know
CRACKING THE GENETIC CODE
By the beginning of the 1960s, the central dogma had
been accepted as the pathway along which information flows from gene to protein. It was clear that genes
encode proteins, that genes are made of DNA, and that
mRNA serves as an intermediary, carrying the information from DNA to the ribosome, where the RNA is
translated into protein.
Even the general format of the genetic code had been
worked out: each of the 20 amino acids found in proteins is represented by a triplet codon in an mRNA
molecule. But an even greater challenge remained:
biologists, chemists, and even physicists set their sights
on breaking the genetic code—attempting to figure out
which amino acid each of the 64 possible nucleotide triplets designates. The most straightforward path to the
solution would have been to compare the sequence of
a segment of DNA or of mRNA with its corresponding
polypeptide product. Techniques for sequencing nucleic
acids, however, would not be devised for another 10
years.
So researchers decided that, to crack the genetic code,
they would have to synthesize their own simple RNA
molecules. If they could feed these RNA molecules to
ribosomes—the machines that make proteins—and
then analyze the resulting polypeptide product, they
would be on their way to deciphering which triplets
encode which amino acids.
Losing the cells
Before researchers could test their synthetic mRNAs,
they needed to perfect a cell-free system for protein
synthesis. This would allow them to translate their
messages into polypeptides in a test tube. (Generally
speaking, when working in the laboratory, the simpler
the system, the easier it is to interpret the results.) To
isolate the molecular machinery they needed for such
a cell-free translation system, researchers broke open
E. coli cells and loaded their contents into a centrifuge
tube. Spinning these samples at high speed caused the
membranes and other large chunks of cellular debris to
be dragged to the bottom of the tube; the lighter cellular
components required for protein synthesis—including
mRNA, the tRNA adaptors, ribosomes, enzymes, and
other small molecules—were left floating in the supernatant. Researchers found that simply adding radioactive
amino acids to this cell “soup” would trigger the production of radiolabeled polypeptides. By centrifuging this
supernatant again, at a higher speed, the researchers
could force the ribosomes, and any newly synthesized
peptides attached to them, to the bottom of the tube; the
labeled polypeptides could then be detected by measuring the radioactivity in the sediment remaining in the
tube after the top layer had been discarded.
The trouble with this particular system was that it
produced proteins encoded by the cell’s own mRNAs
already present in the extract. But researchers wanted
to use their own synthetic messages to direct protein
synthesis. This problem was solved when Marshall
Nirenberg discovered that he could destroy the cells’
mRNA in the extract by adding a small amount of ribonuclease—an enzyme that degrades RNA—to the mix.
Now all he needed to do was prepare large quantities of
synthetic mRNA, add it to the cell-free system, and see
what peptides came out.
Faking the message
Producing a synthetic polynucleotide with a defined
sequence was not as simple as it sounds. Again, it
would be years before chemists and bioengineers developed machines that could synthesize any given string
of nucleic acids quickly and cheaply. Nirenberg decided
to use polynucleotide phosphorylase, an enzyme that
would join ribonucleotides together in the absence of a
template. The sequence of the resulting RNA would then
depend entirely on which nucleotides were presented
to the enzyme. A mixture of nucleotides would be sewn
into a random sequence; but a single type of nucleotide
would yield a homogeneous polymer containing only
that one nucleotide. Thus Nirenberg, working with his
collaborator Heinrich Matthaei, first produced synthetic
mRNAs made entirely of uracil—poly U.
Together, the researchers fed this poly U to their cellfree translation system. They then added a single type
of radioactively labeled amino acid to the mix. After
testing each amino acid—one at a time, in 20 different experiments—they determined that poly U directs
the synthesis of a polypeptide containing only phenylalanine (Figure 7–27). With this electrifying result, the
first word in the genetic code had been deciphered (see
Figure 7–25).
Nirenberg and Matthaei then repeated the experiment
with poly A and poly C and determined that AAA codes
for lysine and CCC for proline. The meaning of poly G
could not be ascertained by this method because this
polynucleotide forms an odd triple-stranded helix that
did not serve as a template in the cell-free system.
Feeding ribosomes with synthetic RNA seemed a
fruitful technique. But with the single-nucleotide possibilities exhausted, researchers had nailed down only
three codons; they had 61 still to go. The other codons,
however, were harder to decipher, and a new synthetic
approach was needed. In the 1950s, the organic chemist Gobind Khorana had been developing methods for
preparing mixed polynucleotides of defined sequence—
but his techniques worked only for DNA. When he
From RNA to Protein
3’
UUUUUUUUUUUUU
UUU
UUUUUUU
5’ U
synthetic mRNA
N
Phe Phe Phe Phe Phe Phe Phe Phe
C
radioactive polypeptide synthesized
241
Figure 7–27 UUU codes for
phenylalanine. Synthetic mRNAs
are fed into a cell-free translation
system containing bacterial
ribosomes, tRNAs, enzymes,
and other small molecules.
Radioactive amino acids are
added to this mix and the
resulting polypeptides analyzed.
In this case, poly U is shown to
encode a polypeptide containing
only phenylalanine.
cell-free translation
system plus radioactive
amino acids
learned of Nirenberg’s work with synthetic RNAs,
Khorana directed his energies and skills to producing
polyribonucleotides. He found that if he started out by
making DNAs of a defined sequence, he could then use
RNA polymerase to produce RNAs from those. In this
ECB4
way, Khorana prepared a collection
of e7.26/7.27
different RNAs
of defined repeating sequence: he generated sequences
of repeating dinucleotides (such as poly UC), trinucleotides (such as poly UUC), or tetranucleotides (such as
poly UAUC).
These mixed polynucleotides, however, yielded results
that were much more difficult to decode than the mononucleotide messages that Nirenberg had used. Take poly
UG, for example. When this repeating dinucleotide is
added to the translation system, researchers discovered
that it codes for a polypeptide of alternating cysteines
and valines. This RNA, of course, contains two different alternating codons: UGU and GUG. So researchers
could say that UGU and GUG code for cysteine and
valine, although they could not tell which went with
which. Thus these mixed messages provided useful
information, but they did not definitively reveal which
codons specified which amino acids (Figure 7–28).
trinucleotides bound to the ribosomes, and Phe-tRNAs
bound to the UUU. The new system was up and running,
and the researchers had confirmed that UUU codes for
phenylalanine.
All that remained was for researchers to produce all 64
possible codons—a task that was quickly accomplished
in both Nirenberg’s and Khorana’s laboratories. Because
these small trinucleotides were much simpler to synthesize chemically, and the triplet-trapping tests were
easier to perform and analyze than the previous decoding experiments, the researchers were able to work out
the complete genetic code within the next year.
MESSAGE
PEPTIDES
PRODUCED
CODON
ASSIGNMENTS
poly UG
...Cys–Val–Cys–Val...
UGU
GUG
Cys, Val*
poly AG
...Arg–Glu–Arg–Glu...
AGA
GAG
Arg, Glu
poly UUC
...Phe–Phe–Phe...
+
...Ser–Ser–Ser...
+
...Leu–Leu–Leu...
UUC
UCU
CUU
Phe, Ser,
Leu
poly UAUC
...Tyr–Leu–Ser–Ile...
UAU
CUA
UCU
AUC
Tyr, Leu,
Ser, Ile
Trapping the triplets
These final ambiguities in the code were resolved when
Nirenberg and a young medical graduate named Phil
Leder discovered that RNA fragments that were only
three nucleotides in length—the size of a single codon—
could bind to a ribosome and attract the appropriate
amino-acid-containing tRNA molecule to the proteinmaking machinery. These complexes—containing one
ribosome, one mRNA codon, and one radiolabeled
aminoacyl-tRNA—could then be captured on a piece of
filter paper and the attached amino acid identified.
Their trial run with UUU—the first word—worked
splendidly. Leder and Nirenberg primed the usual cellfree translation system with snippets of UUU. These
* One codon specifies Cys, the other Val, but which is which?
The same ambiguity exists for the other codon assignments
shown here.
Figure 7–28 Using synthetic RNAs of mixed, repeating
ribonucleotide sequences, scientists further narrowed
the coding possibilities. Although these mixed messages
produced mixed polypeptides, they did not permit the
unambiguous assignment of a single codon to a specific amino
acid. For example, the results of the poly-UG experiment
cannot distinguish whether UGU or GUG encodes cysteine.
As indicated, the same type of ambiguity confounded the
interpretation of all the experiments using di-, tri-, and
ECB4 e7.27/7.28
tetranucleotides.
242
Chapter 7
From DNA to Protein: How Cells Read the Genome
in an mRNA specifies the correct protein. We discuss later how a special
punctuation signal at the beginning of each mRNA molecule sets the correct reading frame.
tRNA Molecules Match Amino Acids to Codons in mRNA
The codons in an mRNA molecule do not directly recognize the amino
acids they specify: the group of three nucleotides does not, for example, bind directly to the amino acid. Rather, the translation of mRNA into
protein depends on adaptor molecules that can recognize and bind to a
codon at one site on their surface and to an amino acid at another site.
These adaptors consist of a set of small RNA molecules known as transfer RNAs (tRNAs), each about 80 nucleotides in length.
We saw earlier that an RNA molecule generally folds into a three-dimensional structure by forming base pairs between different regions of the
molecule. If the base-paired regions are sufficiently extensive, they will
fold back on themselves to form a double-helical structure, like that of
double-stranded DNA. The tRNA molecule provides a striking example of
this. Four short segments of the folded tRNA are double-helical, producing
a molecule that looks like a cloverleaf when drawn schematically (Figure
7–29A). For example, a 5′-GCUC-3′ sequence in one part of a polynucleotide chain can base-pair with a 5′-GAGC-3′ sequence in another region
of the same molecule. The cloverleaf undergoes further folding to form a
compact, L-shaped structure that is held together by additional hydrogen
bonds between different regions of the molecule (Figure 7–29B and C).
Two regions of unpaired nucleotides situated at either end of the L-shaped
tRNA molecule are crucial to the function of tRNAs in protein synthesis.
One of these regions forms the anticodon, a set of three consecutive
nucleotides that bind, through base-pairing, to the complementary codon
attached amino
acid (Phe)
A 3′ end
C
C
A
5′ end G C
C G
G C
G U
A U
U A
C U A
U A
GAC AC
U
G
A
D GA
C
D
CUC G
CCU G UG T
Ψ
U
G
G
G G A G A GC G
G
C GA
C G
A U
G C
A
Ψ anticodon
A
C
loop
U
Y
GA A
anticodon
a cloverleaf
(A)
(B)
(C)
(D)
5 ′ GCGGAUUUAGCUCAGDDGGGAGAGCGCCAGACUGAAYAΨCUGGAGGUCCUGUGTΨCGAUCCACAGAAUUCGCACCA 3′
(E)
anticodon
Figure 7–29 tRNA molecules are molecular adaptors, linking amino acids to codons. In this series of diagrams, the same tRNA
molecule—in this case, a tRNA specific for the amino acid phenylalanine (Phe)—is depicted in various ways. (A) The conventional
“cloverleaf” structure shows the complementary base-pairing (red lines) that creates the double-helical regions of the molecule. The
anticodon loop (blue) contains the sequence of three nucleotides (red letters) that base-pairs with a codon in mRNA. The amino acid
matching the codon–anticodon pair is attached at the 3′ end of the tRNA. tRNAs contain some unusual bases, which are produced by
chemical modification after the tRNA has been synthesized. The bases denoted Ψ (for pseudouridine) and D (for dihydrouridine) are
derived from uracil. (B and C) Views of the actual L-shaped molecule, based on X-ray diffraction analysis. These two images are rotated
90º with respect to each other. (D) Schematic
representation of tRNA, emphasizing the anticodon, that will be used in subsequent
ECB4 e7.28/7.29
figures. (E) The linear nucleotide sequence of the tRNA molecule, color-coded to match A, B, and C.
From RNA to Protein
243
in an mRNA molecule. The other is a short single-stranded region at the
3′ end of the molecule; this is the site where the amino acid that matches
the codon is covalently attached to the tRNA.
We saw in the previous section that the genetic code is redundant; that
is, several different codons can specify a single amino acid (see Figure
7–25). This redundancy implies either that there is more than one tRNA
for many of the amino acids or that some tRNA molecules can base-pair
with more than one codon. In fact, both situations occur. Some amino
acids have more than one tRNA, and some tRNAs are constructed so
that they require accurate base-pairing only at the first two positions of
the codon and can tolerate a mismatch (or wobble) at the third position.
This wobble base-pairing explains why so many of the alternative codons
for an amino acid differ only in their third nucleotide (see Figure 7–25).
Wobble base-pairings make it possible to fit the 20 amino acids to their
61 codons with as few as 31 kinds of tRNA molecules. The exact number
of different kinds of tRNAs, however, differs from one species to the next.
For example, humans have nearly 500 different tRNA genes, but only 48
anticodons are represented among them.
Specific Enzymes Couple tRNAs to the Correct Amino
Acid
For a tRNA molecule to carry out its role as an adaptor, it must be linked—
or charged—with the correct amino acid. How does each tRNA molecule
recognize the one amino acid in 20 that is its right partner? Recognition
and attachment of the correct amino acid depend on enzymes called
aminoacyl-tRNA synthetases, which covalently couple each amino acid
to its appropriate set of tRNA molecules. In most organisms, there is a
different synthetase enzyme for each amino acid. That means that there
are 20 synthetases in all: one attaches glycine to all tRNAs that recognize codons for glycine, another attaches phenylalanine to all tRNAs that
recognize codons for phenylalanine, and so on. Each synthetase enzyme
recognizes specific nucleotides in both the anticodon and the aminoacid-accepting arm of the correct tRNA (Movie 7.6). The synthetases are
thus equal in importance to the tRNAs in the decoding process, because
it is the combined action of the synthetases and tRNAs that allows each
codon in the mRNA molecule to specify its proper amino acid (Figure
7–30).
amino acid
(tryptophan)
H
H2N
C
H
O
C
H2N
OH
tRNA
Trp
(tRNA )
CH2
N
H
H
O
C
high-energy
bond
O
H2N
O
C
CH2
C
C
C
C
CH
CH
N
H
A
C
C
O
CH2
CH
ATP
tRNA synthetase
(tryptophanyl
tRNA synthetase)
C
Figure 7–30 The genetic code is
translated by the cooperation of two
adaptors: aminoacyl-tRNA synthetases
and tRNAs. Each synthetase couples a
particular amino acid to its corresponding
tRNAs, a process called charging. The
anticodon on the charged tRNA molecule
then forms base pairs with the appropriate
codon on the mRNA. An error in either
the charging step or the binding of the
charged tRNA to its codon will cause the
wrong amino acid to be incorporated into
a protein chain. In the sequence of events
shown, the amino acid tryptophan (Trp) is
selected by the codon UGG on the mRNA.
N
H
AMP + 2 Pi
LINKAGE OF AMINO
ACID TO tRNA
A
C
C
ANTICODON IN tRNA
BINDS TO ITS CODON
IN mRNA
5′
3′ A
C
U
G
anticodon
in tRNA
C 5′
base-pairing
G
codon in
3′
mRNA
NET RESULT: AMINO ACID IS
SELECTED BY ITS CODON IN
AN mRNA
244
Chapter 7
From DNA to Protein: How Cells Read the Genome
The synthetase-catalyzed reaction that attaches the amino acid to the 3′
end of the tRNA is one of many reactions in cells coupled to the energyreleasing hydrolysis of ATP (see Figure 3–33). The reaction produces a
high-energy bond between the charged tRNA and the amino acid. The
energy of this bond is later used to link the amino acid covalently to the
growing polypeptide chain.
The mRNA Message Is Decoded by Ribosomes
Question 7–4
In a clever experiment performed in
1962, a cysteine already attached to
its tRNA was chemically converted
to an alanine. These “hybrid” tRNA
molecules were then added to a cellfree translation system from which
the normal cysteine-tRNAs had
been removed. When the resulting
protein was analyzed, it was found
that alanine had been inserted at
every point in the polypeptide chain
where cysteine was supposed to be.
Discuss what this experiment tells
you about the role of aminoacyltRNA synthetases during the normal
translation of the genetic code.
The recognition of a codon by the anticodon on a tRNA molecule depends
on the same type of complementary base-pairing used in DNA replication
and transcription. However, accurate and rapid translation of mRNA into
protein requires a molecular machine that can move along the mRNA,
capture complementary tRNA molecules, hold the tRNAs in position, and
then covalently link the amino acids that they carry to form a polypeptide
chain. In both prokaryotes and eukaryotes, the machine that gets the job
done is the ribosome—a large complex made from dozens of small proteins (the ribosomal proteins) and several crucial RNA molecules called
ribosomal RNAs (rRNAs). A typical eukaryotic cell contains millions of
ribosomes in its cytoplasm (Figure 7–31).
Eukaryotic and prokaryotic ribosomes are very similar in structure and
function. Both are composed of one large subunit and one small subunit,
which fit together to form a complete ribosome with a mass of several
million daltons (Figure 7–32); for comparison, an average-sized protein has a mass of 30,000 daltons. The small ribosomal subunit matches
the tRNAs to the codons of the mRNA, while the large subunit catalyzes
the formation of the peptide bonds that covalently link the amino acids
together into a polypeptide chain. These two subunits come together on
an mRNA molecule near its 5′ end to start the synthesis of a protein. The
mRNA is then pulled through the ribosome like a long piece of tape. As
the mRNA inches forward in a 5′-to-3′ direction, the ribosome translates
its nucleotide sequence into an amino acid sequence, one codon at a
time, using the tRNAs as adaptors. Each amino acid is thereby added in
the correct sequence to the end of the growing polypeptide chain (Movie
7.7). When synthesis of the protein is finished, the two subunits of the
ribosome separate. Ribosomes operate with remarkable efficiency: a
eukaryotic ribosome adds about 2 amino acids to a polypeptide chain
each second; a bacterial ribosome operates even faster, adding about 20
amino acids per second.
endoplasmic reticulum
Figure 7–31 Ribosomes are located in
the cytoplasm of eukaryotic cells. This
electron micrograph shows a thin section of
a small region of cytoplasm. The ribosomes
appear as small gray blobs. Some are free in
the cytosol (red arrows); others are attached
to membranes of the endoplasmic reticulum
(green arrows). (Courtesy of George Palade.)
cytosol
400 nm
From RNA to Protein
+
rRNA
+
rRNA
+
rRNA
~49 ribosomal proteins + 3 rRNA molecules
large subunit
+
245
Figure 7–32 The eukaryotic ribosome
is a large complex of four rRNAs and
more than 80 small proteins. Prokaryotic
ribosomes are very similar: both are formed
from a large and small subunit, which only
come together after the small subunit has
bound an mRNA. Although ribosomal
proteins greatly outnumber rRNAs, the
RNAs account for most of the mass of the
ribosome and give it its overall shape and
structure.
rRNA
~33 ribosomal proteins + 1 rRNA molecule
small subunit
MW = 1,400,000
MW = 2,800,000
large
subunit
small
subunit
~82 different proteins +
4 different rRNA molecules
complete eukaryotic ribosome
MW = 4,200,000
ECB4 e7.31/7.32
How does the ribosome choreograph
all the movements required for
translation? In addition to a binding site for an mRNA molecule, each
ribosome contains three binding sites for tRNA molecules, called the A
site, the P site, and the E site (Figure 7–33). To add an amino acid to a
growing peptide chain, the appropriate charged tRNA enters the A site
by base-pairing with the complementary codon on the mRNA molecule.
Its amino acid is then linked to the peptide chain held by the tRNA in the
neighboring P site. Next, the large ribosomal subunit shifts forward, moving the spent tRNA to the E site before ejecting it (Figure 7–34). This cycle
of reactions is repeated each time an amino acid is added to the polypeptide chain, with the new protein growing from its amino to its carboxyl
end until a stop codon in the mRNA is encountered.
E site
P site
A site
large
ribosomal
subunit
E
P
small
ribosomal
subunit
mRNAbinding site
(A)
(B)
A
Figure 7–33 Each ribosome has a binding
site for mRNA and three binding sites
for tRNA. The tRNA sites are designated
the A, P, and E sites (short for aminoacyltRNA, peptidyl-tRNA, and exit, respectively).
(A) Three-dimensional structure of a
bacterial ribosome, as determined by X-ray
crystallography, with the small subunit in
dark green and the large subunit in light
green. Both the rRNAs and the ribosomal
proteins are shown in green. tRNAs are
shown bound in the E site (red), the P site
(orange), and the A site (yellow). Although
all three tRNA sites are shown occupied
here, during the process of protein synthesis
only two of these sites are occupied at
any one time (see Figure 7–34). (B) Highly
schematized representation of a ribosome
(in the same orientation as A), which will be
used in subsequent figures. Note that both
the large and small subunits are involved
in forming the A, P, and E sites, while only
the small subunit forms the binding site for
an mRNA. (B, adapted from M.M. Yusupov
et al., Science 292:883–896, 2001, with
permission from AAAS. Courtesy of Albion
Baucom and Harry Noller.)
246
Chapter 7
From DNA to Protein: How Cells Read the Genome
growing polypeptide chain
STEP 1
2
1
H2N
E
3
newly bound
charged
tRNA
4
P
3
A
4
5′
3′
E site
P site
STEP 2
2
3
1
H2N
A site
4
E
P
3
A
4
5′
3′
STEP 3
LARGE SUBUNIT TRANSLOCATES
2
3
1
H2N
4
3
P
4
The Ribosome Is a Ribozyme
A
5′
3′
STEP 4
2
3
1
H2 N
4
3
4
ejected tRNA
5′
A
3′
SMALL SUBUNIT TRANSLOCATES
STEP 1
2
H 2N
3
1
E
5′
4
5
4
5
Figure 7–34 Translation takes place in a four-step cycle. This cycle
is repeated over and over during the synthesis of a protein. In step
1, a charged tRNA carrying the next amino acid to be added to the
polypeptide chain binds to the vacant A site on the ribosome by forming
base pairs with the mRNA codon that is exposed there. Because only
the appropriate tRNA molecules can base-pair with each codon, this
codon determines the specific amino acid added. The A and P sites are
sufficiently close together that their two tRNA molecules are forced to
form base pairs with codons that are contiguous, with no stray bases in
between. This positioning of the tRNAs ensures that the correct reading
frame will be preserved throughout the synthesis of the protein. In step
2, the carboxyl end of the polypeptide chain (amino acid 3 in step 1) is
uncoupled from the tRNA at the P site and joined by a peptide bond to
the free amino group of the amino acid linked to the tRNA at the A site.
This reaction is catalyzed by an enzymatic site in the large subunit. In
step 3, a shift of the large subunit relative to the small subunit moves the
two tRNAs into the E and P sites of the large subunit. In step 4, the small
subunit moves exactly three nucleotides along the mRNA molecule,
bringing it back to its original position relative to the large subunit. This
movement ejects the spent tRNA and resets the ribosome with an empty
A site so that the next charged tRNA molecule can bind (Movie 7.8).
As indicated, the mRNA is translated in the 5′-to-3′ direction, and the
N-terminal end of a protein is made first, with each cycle adding one
amino acid to the C-terminus of the polypeptide chain. To watch the
translation cycle in atomic detail, see Movie 7.9.
The ribosome is one of the largest and most complex structures in the cell,
composed of two-thirds RNA and one-third protein by weight. The determination of the entire three-dimensional structure of its large and small
subunits in 2000 was a major triumph of modern biology. The structure
confirmed earlier evidence that the rRNAs—not the proteins—are responsible for the ribosome’s overall structure and its ability to choreograph
and catalyze protein synthesis.
The rRNAs are folded into highly compact, precise three-dimensional
structures that form the core of the ribosome (Figure 7–35). In marked
contrast to the central positioning of the rRNAs, the ribosomal proteins
are generally located on the surface, where they fill the gaps and crevices
of the folded RNA. The main role of the ribosomal proteins seems to be
newly
bound
charged
tRNA
5S rRNA
3′
Figure 7–35 Ribosomal RNAs give the
ribosome its overall shape. Shown here
are the detailed structures of the two rRNAs
that form the core of the large subunit of
a bacterial ribosome—the 23S rRNA (blue)
and the 5S rRNA (purple). One of the protein
subunits of the ribosome (L1) is included
as a reference point, as this protein forms
a characteristic protrusion on the ribosome
surface. Ribosomal components
are commonly
ECB4 e7.33/7.34
designated by their “S values,” which
refer to their rate of sedimentation in an
ultracentrifuge. (Adapted from N. Ban et al.,
Science 289:905–920, 2000. With permission
from AAAS.)
L1
23S rRNA
247
From RNA to Protein
to help fold and stabilize the RNA core, while permitting the changes in
rRNA conformation that are necessary for this RNA to catalyze efficient
protein synthesis.
Question 7–5
A sequence of nucleotides in a DNA
strand—5′-TTAACGGCTTTTTTC-3′—
was used as a template to
synthesize an mRNA that was then
translated into protein. Predict
the C-terminal amino acid and
the N-terminal amino acid of the
resulting polypeptide. Assume that
the mRNA is translated without the
need for a start codon.
Not only are the three tRNA-binding sites (the A, P, and E sites) on the
ribosome formed primarily by the rRNAs, but the catalytic site for peptide
bond formation is formed by the 23S rRNA of the large subunit; the nearest ribosomal protein is located too far away to make contact with the
incoming charged tRNA or with the growing polypeptide chain. The catalytic site in this rRNA—a peptidyl transferase—is similar in many respects
to that found in some protein enzymes: it is a highly structured pocket
that precisely orients the two reactants—the elongating polypeptide and
the charged tRNA—thereby greatly increasing the probability of a productive reaction.
RNA molecules that possess catalytic activity are called ribozymes. Later,
in the final section of this chapter, we will consider other ribozymes and
discuss what the existence of RNA-based catalysis might mean for the
early evolution of life on Earth. Here we need only note that there is good
reason to suspect that RNA rather than protein molecules served as the
first catalysts for living cells. If so, the ribosome, with its catalytic RNA
core, could be viewed as a relic of an earlier time in life’s history, when
cells were run almost entirely by ribozymes.
translation initiation
factors
Met
initiator tRNA
small ribosomal subunit
with translation initiation
factors bound
Met
mRNA BINDING
Specific Codons in mRNA Signal the Ribosome Where to
Start and to Stop Protein Synthesis
In the test tube, ribosomes can be forced to translate any RNA molecule
(see How We Know, pp. 240–241). In a cell, however, a specific start signal is required to initiate translation. The site at which protein synthesis
begins on an mRNA is crucial, because it sets the reading frame for the
whole length of the message. An error of one nucleotide either way at
this stage will cause every subsequent codon in the mRNA to be misread,
resulting in a nonfunctional protein with a garbled sequence of amino
acids (see Figure 7–26). And the rate of initiation determines the rate at
which the protein is synthesized from the mRNA.
The translation of an mRNA begins with the codon AUG, and a special
charged tRNA is required to initiate translation. This initiator tRNA
always carries the amino acid methionine (or a modified form of methionine, formyl-methionine, in bacteria). Thus newly made proteins all have
methionine as the first amino acid at their N-terminal end, the end of a
protein that is synthesized first. This methionine is usually removed later
by a specific protease.
P
mRNA
5′
AUG
SMALL RIBOSOMAL
SUBUNIT, WITH BOUND
INITIATOR tRNA,
MOVES ALONG
mRNA SEARCHING
FOR FIRST AUG
Met
P
5′
3′
AUG
TRANSLATION
INITIATION
FACTORS
DISSOCIATE
LARGE
RIBOSOMAL
SUBUNIT
BINDS
Met
E
5′
In eukaryotes, an initiator tRNA, charged with methionine, is first loaded
into the P site of the small ribosomal subunit, along with additional proteins called translation initiation factors (Figure 7–36). The initiator
tRNA is distinct from the tRNA that normally carries methionine. Of all
the tRNAs in the cell, only a charged initiator tRNA molecule is capable of
binding tightly to the P site in the absence of the large ribosomal subunit.
Next, the small ribosomal subunit loaded with the initiator tRNA binds to
P
A
3′
AUG
aa
Met aa
E
5′
Figure 7–36 Initiation of protein synthesis in eukaryotes requires
translation initiation factors and a special initiator tRNA. Although
not shown here, efficient translation initiation also requires additional
proteins that are bound at the 5′ cap and poly-A tail of the mRNA
(see Figure 7–23). In this way, the translation apparatus can ascertain
that both ends of the mRNA are intact before initiating translation.
Following initiation, the protein is elongated by the reactions outlined
in Figure 7–34.
3′
P
CHARGED
tRNA BINDS
TO A SITE
(step 1)
A
3′
AUG
FIRST PEPTIDE
BOND FORMS
(step 2)
Met
E
5′
P
AUG
aa
A
3′
248
Chapter 7
From DNA to Protein: How Cells Read the Genome
ribosome-binding sites
5′
3′
P P P
AUG
protein α
AUG
mRNA
AUG
protein β
protein γ
Figure 7–37 A single prokaryotic mRNA molecule can encode several different
proteins. In prokaryotes, genes directing the different steps in a process are often
organized into clusters (operons) that are transcribed together into a single mRNA.
A prokaryotic mRNA does not have the same sort of 5′ cap as a eukaryotic mRNA,
but instead has a triphosphate at its 5′ end. Prokaryotic ribosomes initiate translation
at ribosome-binding sites (dark blue), which can be located in the interior of an
mRNA molecule. This feature enables prokaryotes to synthesize different proteins
ECB4
e7.36/7.37
from a single mRNA molecule, with
each
protein made by a different ribosome.
H2N
E
P
terminal
portion of
mRNA
A
UAG
5′
3′
BINDING OF
RELEASE
FACTOR
TO THE
A SITE
H2N
E
P
UAG
5′
3′
H2O
released
polypeptide
chain
NH2
COOH
TERMINATION
P
A
UAG
5′
3′
RIBOSOME
DISSOCIATES
the 5′ end of an mRNA molecule, which is marked by the 5′ cap that is
present on all eukaryotic mRNAs (see Figure 7–16). The small ribosomal
subunit then moves forward (5′ to 3′) along the mRNA searching for the
first AUG. When this AUG is encountered and recognized by the initiator
tRNA, several initiation factors dissociate from the small ribosomal subunit to make way for the large ribosomal subunit to bind and complete
ribosomal assembly. Because the initiator tRNA is bound to the P site,
protein synthesis is ready to begin with the addition of the next charged
tRNA to the A site (see Figure 7–34).
The mechanism for selecting a start codon is different in bacteria. Bacterial
mRNAs have no 5′ caps to tell the ribosome where to begin searching for
the start of translation. Instead, they contain specific ribosome-binding
sequences, up to six nucleotides long, that are located a few nucleotides
upstream of the AUGs at which translation is to begin. Unlike a eukaryotic ribosome, a prokaryotic ribosome can readily bind directly to a start
codon that lies in the interior of an mRNA, as long as a ribosome-binding
site precedes it by several nucleotides. Such ribosome-binding sequences
are necessary in bacteria, as prokaryotic mRNAs are often polycistronic—
that is, they encode several different proteins, each of which is translated
from the same mRNA molecule (Figure 7–37). In contrast, a eukaryotic
mRNA usually carries the information for a single protein.
The end of translation in both prokaryotes and eukaryotes is signaled by
the presence of one of several codons, called stop codons, in the mRNA
(see Figure 7–25). The stop codons—UAA, UAG, and UGA—are not recognized by a tRNA and do not specify an amino acid, but instead signal to
the ribosome to stop translation. Proteins known as release factors bind
to any stop codon that reaches the A site on the ribosome; this binding
alters the activity of the peptidyl transferase in the ribosome, causing it to
catalyze the addition of a water molecule instead of an amino acid to the
peptidyl-tRNA (Figure 7–38). This reaction frees the carboxyl end of the
polypeptide chain from its attachment to a tRNA molecule; because this
is the only attachment that holds the growing polypeptide to the ribosome, the completed protein chain is immediately released. At this point,
the ribosome also releases the mRNA and dissociates into its two separate subunits, which can then assemble on another mRNA molecule to
begin a new round of protein synthesis.
UAG
5′
3′
Figure 7–38 Translation halts at a stop codon. In the final phase of
protein synthesis, the binding of release factor to an A site bearing
a stop codon terminates translation of an mRNA molecule. The
completed polypeptide is released, and the ribosome dissociates
into its two separate subunits. Note that only the 3ʹ end of the mRNA
molecule is shown here.
From RNA to Protein
249
We saw in Chapter 4 that many proteins can fold into their three-dimensional shape spontaneously, and some do so as they are spun out of the
ribosome. Most proteins, however, require chaperone proteins to help
them fold correctly in the cell. Chaperones can “steer” proteins along productive folding pathways and prevent them from aggregating inside the
cell (see Figures 4–9 and 4–10). Newly synthesized proteins are typically
met by their chaperones as they emerge from the ribosome.
Proteins Are Made on Polyribosomes
The synthesis of most protein molecules takes between 20 seconds and
several minutes. But even during this short period, multiple ribosomes
usually bind to each mRNA molecule being translated. If the mRNA is
being translated efficiently, a new ribosome hops onto the 5′ end of the
mRNA molecule almost as soon as the preceding ribosome has translated enough of the nucleotide sequence to move out of the way. The
mRNA molecules being translated are therefore usually found in the form
of polyribosomes, also known as polysomes. These large cytoplasmic
assemblies are made up of many ribosomes spaced as close as 80 nucleotides apart along a single mRNA molecule (Figure 7–39). With multiple
ribosomes working simultaneously on a single mRNA, many more protein molecules can be made in a given time than would be possible if
each polypeptide had to be completed before the next could be started.
Polysomes operate in both bacteria and eukaryotes, but bacteria can
speed up the rate of protein synthesis even further. Because bacterial
mRNA does not need to be processed and is also physically accessible to
ribosomes while it is being made, ribosomes will typically attach to the
free end of a bacterial mRNA molecule and start translating it even before
the transcription of that RNA is complete; these ribosomes follow closely
behind the RNA polymerase as it moves along DNA.
Inhibitors of Prokaryotic Protein Synthesis Are Used as
Antibiotics
The ability to translate mRNAs accurately into proteins is a fundamental
feature of all life on Earth. Although the ribosome and other molecules
that carry out this complex task are very similar among organisms, we
A3
AA
AA
′
G
UA
stop
codon
5′
AUG
start
codon
mRNA
growing
polypeptide
chain
(A)
100 nm
(B)
100 nm
Figure 7–39 Proteins are synthesized on
polyribosomes. (A) Schematic drawing
showing how a series of ribosomes can
simultaneously translate the same mRNA
molecule (Movie 7.10). (B) Electron
micrograph of a polyribosome in the cytosol
of a eukaryotic cell. (B, courtesy of John
Heuser.)
250
Chapter 7
From DNA to Protein: How Cells Read the Genome
Table 7–3 Antibiotics that Inhibit BACTERIAL Protein or RNA
Synthesis
Antibiotic
Specific Effect
Tetracycline
blocks binding of aminoacyl-tRNA to A site of ribosome
(step 1 in Figure 7–34)
Streptomycin
prevents the transition from initiation complex to chain
elongation (see Figure 7–36); also causes miscoding
Chloramphenicol
blocks the peptidyl transferase reaction on ribosomes
(step 2 in Figure 7–34)
Cycloheximide
blocks the translocation reaction on ribosomes (step 3 in
Figure 7–34)
Rifamycin
blocks initiation of transcription by binding to RNA
polymerase
have seen that there are some subtle differences in the way that bacteria and eukaryotes synthesize RNA and proteins. Through a quirk of
evolution, these differences form the basis of one of the most important
advances in modern medicine.
Many of our most effective antibiotics are compounds that act by inhibiting bacterial, but not eukaryotic, RNA and protein synthesis. Some
of these drugs exploit the small structural and functional differences
between bacterial and eukaryotic ribosomes, so that they interfere preferentially with bacterial protein synthesis. These compounds can thus
be taken in doses high enough to kill bacteria without being toxic to
humans. Because different antibiotics bind to different regions of the
bacterial ribosome, these drugs often inhibit different steps in protein
synthesis. A few of the antibiotics that inhibit bacterial RNA and protein
synthesis are listed in Table 7–3.
Many common antibiotics were first isolated from fungi. Fungi and bacteria often occupy the same ecological niches; to gain a competitive edge,
fungi have evolved, over time, potent toxins that kill bacteria but are
harmless to themselves. Because fungi and humans are both eukaryotes,
and are thus more closely related to each other than either is to bacteria
(see Figure 1–28), we have been able to borrow these weapons to combat
our own bacterial foes.
Controlled Protein Breakdown Helps Regulate the Amount
of Each Protein in a Cell
After a protein is released from the ribosome, a cell can control its activity and longevity in various ways. The number of copies of a protein in
a cell depends, like the human population, not only on how quickly new
individuals are made but also on how long they survive. So controlling
the breakdown of proteins into their constituent amino acids helps cells
regulate the amount of each particular protein. Proteins vary enormously
in their life-span. Structural proteins that become part of a relatively stable tissue such as bone or muscle may last for months or even years,
whereas other proteins, such as metabolic enzymes and those that regulate cell growth and division (discussed in Chapter 18), last only for days,
hours, or even seconds. How does the cell control these lifetimes?
Cells possess specialized pathways that enzymatically break proteins
down into their constituent amino acids (a process termed proteolysis).
The enzymes that degrade proteins, first to short peptides and finally to
individual amino acids, are known collectively as proteases. Proteases
From RNA to Protein
(A)
251
Figure 7–40 A proteasome degrades
short-lived and misfolded proteins. The
structures shown were determined by X-ray
crystallography. (A) A cut-away view of the
central cylinder of the proteasome, with
the active sites of the proteases indicated
by red dots. (B) The structure of the entire
proteasome, in which access to the central
cylinder (yellow) is regulated by a stopper
(blue) at each end. (B, adapted from P.C.A
da Fonseca et al., Mol. Cell 46:54–66, 2012.)
(B)
act by cutting (hydrolyzing) the peptide bonds between amino acids (see
Panel 2–5, pp. 74–75). One function of proteolytic pathways is to rapidly degrade those proteins whose lifetimes must be kept short. Another
is to recognize and remove proteins that are damaged or misfolded.
Eliminating improperly folded proteins is critical for an organism, as misfolded proteins tend to aggregate, and protein aggregates can damage
cells and even trigger cell death. Eventually, all proteins—even long-lived
ECB4 e7.39/7.40
ones—accumulate damage and are degraded by proteolysis.
In eukaryotic cells, proteins are broken down by large protein machines
called proteasomes, present in both the cytosol and the nucleus. A proteasome contains a central cylinder formed from proteases whose active
sites face into an inner chamber. Each end of the cylinder is stoppered by
a large protein complex formed from at least 10 types of protein subunits
(Figure 7–40). These protein stoppers bind the proteins destined for degradation and then—using ATP hydrolysis to fuel this activity—unfold the
doomed proteins and thread them into the inner chamber of the cylinder.
Once the proteins are inside, proteases chop them into short peptides,
which are then jettisoned from either end of the proteasome. Housing
proteases inside these molecular destruction chambers makes sense, as
it prevents the enzymes from running rampant in the cell.
How do proteasomes select which proteins in the cell should be degraded?
In eukaryotes, proteasomes act primarily on proteins that have been
marked for destruction by the covalent attachment of a small protein
called ubiquitin. Specialized enzymes tag selected proteins with a short
chain of ubiquitin molecules; these ubiquitylated proteins are then recognized, unfolded, and fed into proteasomes by proteins in the stopper
(Figure 7–41).
target protein with
polyubiquitin chain
central
cylinder
(proteases)
stopper
active sites
UBIQUITIN
RECYCLED
PROTEIN
DEGRADED
Figure 7–41 Proteins marked by a
polyubiquitin chain are degraded by the
proteasome. Proteins in the stopper of a
proteasome (blue) recognize target proteins
marked by a specific type of polyubiquitin
chain. The stopper then unfolds the target
protein and threads it into the proteasome’s
central cylinder (yellow), which is lined with
proteases that chop the protein to pieces.
252
Chapter 7
From DNA to Protein: How Cells Read the Genome
Proteins that are meant to be short-lived often contain a short amino
acid sequence that identifies the protein as one to be ubiquitylated and
degraded in proteasomes. Damaged or misfolded proteins, as well as
proteins containing oxidized or otherwise abnormal amino acids, are
also recognized and degraded by this ubiquitin-dependent proteolytic
system. The enzymes that add a polyubiquitin chain to such proteins recognize signals that become exposed on these proteins as a result of the
misfolding or chemical damage—for example, amino acid sequences or
conformational motifs that remain buried and inaccessible in the normal
“healthy” protein.
There Are Many Steps Between DNA and Protein
We have seen that many types of chemical reactions are required to
produce a protein from the information contained in a gene. The final
concentration of a protein in a cell therefore depends on the rate at which
each of the many steps is carried out (Figure 7–42). In addition, many
proteins—once they leave the ribosome—require further attention before
they are useful to the cell. Examples of such post-translational modifications include covalent modification (such as phosphorylation), the binding
of small-molecule cofactors, or association with other protein subunits,
which are often needed for a newly synthesized protein to become fully
functional (Figure 7–43).
exons
introns
5′
3′
DNA
INITIATION OF TRANSCRIPTION
5′ RNA CAPPING,
ELONGATION,
AND SPLICING
5′ cap
3′ RNA CLEAVAGE,
POLYADENYLATION,
AND TERMINATION OF TRANSCRIPTION
AAAA
EXPORT
mRNA
poly-A tail
NUCLEUS
CYTOSOL
AAAA
mRNA
mRNA DEGRADATION
Figure 7–42 Protein production in a
eukaryotic cell requires many steps. The
final concentration of each protein depends
on the rate of each step depicted. Even after
an mRNA and its corresponding protein have
been produced, their concentrations can
be regulated by degradation. Although not
shown here, the activity of the protein can
also be regulated by other post-translational
modifications or the binding of small
molecules (see Figure 7–43).
INITIATION OF PROTEIN SYNTHESIS (TRANSLATION)
AAAA
COMPLETION OF PROTEIN SYNTHESIS
AND PROTEIN FOLDING
H2N
COOH
PROTEIN DEGRADATION
H2N
COOH
RNA and the Origins of Life
We will see in the next chapter that cells have the ability to change the
concentrations of most of their proteins according to their needs. In principle, all of the steps in Figure 7–42 can be regulated by the cell—and
many of them, in fact, are. However, as we will see in the next chapter,
the initiation of transcription is the most common point for a cell to regulate the expression of its genes.
Transcription and translation are universal processes that lie at the heart
of life. However, when scientists came to consider how the flow of information from DNA to protein might have originated, they came to some
unexpected conclusions.
RNA and the Origins of Life
The central dogma—that DNA makes RNA that makes protein—presented
evolutionary biologists with a knotty puzzle: if nucleic acids are required
to direct the synthesis of proteins, and proteins are required to synthesize nucleic acids, how could this system of interdependent components
have arisen? One view is that an RNA world existed on Earth before
cells containing DNA and proteins appeared. According to this hypothesis, RNA—which today serves largely as an intermediate between genes
and proteins—both stored genetic information and catalyzed chemical
reactions in primitive cells. Only later in evolutionary time did DNA take
over as the genetic material and proteins become the major catalysts
and structural components of cells (Figure 7–44). If this idea is correct,
then the transition out of the RNA world was never completed; as we
have seen, RNA still catalyzes several fundamental reactions in modern
cells. These RNA catalysts—or ribozymes—including those that operate
in the ribosome and in the RNA-splicing machinery, can thus be viewed
as molecular fossils of an earlier world.
Life Requires Autocatalysis
The origin of life requires molecules that possess, if only to a small extent,
one crucial property: the ability to catalyze reactions that lead—directly or
indirectly—to the production of more molecules like themselves. Catalysts
with this self-producing property, once they had arisen by chance, would
divert raw materials from the production of other substances to make
more of themselves. In this way, one can envisage the gradual development of an increasingly complex chemical system of organic monomers
and polymers that function together to generate more molecules of the
same types, fueled by a supply of simple raw materials in the primitive
environment on Earth. Such an autocatalytic system would have many
of the properties we think of as characteristic of living matter: the system would contain a far-from-random selection of interacting molecules;
it would tend to reproduce itself; it would compete with other systems
dependent on the same raw materials; and, if deprived of its raw materials or maintained at a temperature that upset the balance of reaction
rates, it would decay toward chemical equilibrium and “die.”
solar
system
formed
Big Bang
first cells
with DNA
nascent polypeptide chain
FOLDING AND
COFACTOR BINDING,
DEPENDENT ON
NONCOVALENT
INTERACTIONS
COVALENT MODIFICATION
BY, FOR EXAMPLE,
PHOSPHORYLATION
P
NONCOVALENT BINDING
TO OTHER PROTEIN
SUBUNIT
P
mature functional protein
Figure 7–43 Many proteins require
various modifications to become fully
functional. To be useful to the cell, a
completed polypeptide must fold correctly
into its three-dimensional conformation
and then bind any required cofactors (red)
ECB4 e7.41/7.43
and protein partners—all via noncovalent
bonding. Many proteins also require one
or more covalent modifications to become
active—or to be recruited to specific
membranes or organelles (not shown).
Although phosphorylation and glycosylation
are the most common, more than 100 types
of covalent modifications of proteins are
known.
first
mammals
present
14
10
time (billions of years ago)
5
RNA
WORLD
253
Figure 7–44 An RNA world may have
existed before modern cells with DNA
and proteins evolved.
254
Chapter 7
From DNA to Protein: How Cells Read the Genome
But what molecules could have had such autocatalytic properties? In
present-day living cells, the most versatile catalysts are proteins, which
are able to adopt diverse three-dimensional forms that bristle with chemically reactive sites on their surface. However, there is no known way in
which a protein can reproduce itself directly. RNA molecules, by contrast,
could—at least, in principle—catalyze their own synthesis.
RNA Can Both Store Information and Catalyze Chemical
Reactions
We have seen that complementary base-pairing enables one nucleic acid
to act as a template for the formation of another. Thus a single strand of
RNA or DNA can specify the sequence of a complementary polynucleotide, which, in turn, can specify the sequence of the original molecule,
allowing the original nucleic acid to be replicated (Figure 7–45). Such
complementary templating mechanisms lie at the heart of both DNA replication and transcription in modern-day cells.
But the efficient synthesis of polynucleotides by such complementary
templating mechanisms also requires catalysts to promote the polymerization reaction: without catalysts, polymer formation is slow, error-prone,
and inefficient. Today, nucleotide polymerization is catalyzed by protein
enzymes—such as DNA and RNA polymerases. But how could this reaction be catalyzed before proteins with the appropriate catalytic ability
existed? The beginnings of an answer were obtained in 1982, when it
was discovered that RNA molecules themselves can act as catalysts. The
unique potential of RNA molecules to act both as information carriers
and as catalysts is thought to have enabled them to have a central role
in the origin of life.
In present-day cells, RNA is synthesized as a single-stranded molecule,
and we have seen that complementary base-pairing can occur between
nucleotides in the same chain. This base-pairing, along with nonconventional hydrogen bonds, can cause each RNA molecule to fold up in
a unique way that is determined by its nucleotide sequence (see Figure
7–5). Such associations produce complex three-dimensional shapes.
As we discuss in Chapter 4, protein enzymes are able to catalyze biochemical reactions because they have surfaces with unique contours
and chemical properties. In the same way, RNA molecules, with their
unique folded shapes, can serve as catalysts (Figure 7–46). RNAs do not
have the same structural and functional diversity as do protein enzymes;
they are, after all, built from only four different subunits. Nonetheless,
ribozymes can catalyze many types of chemical reactions. Most of the
ribozymes that have been studied were constructed in the laboratory and
selected for their catalytic activity in a test tube (Table 7–4), as relatively
few catalytic RNAs exist in present-day cells. But the processes in which
catalytic RNAs still seem to have major roles include some of the most
Figure 7–45 An RNA molecule can in
principle guide the formation of an
exact copy of itself. In the first step, the
original RNA molecule acts as a template to
form an RNA molecule of complementary
sequence. In the second step, this
complementary RNA molecule itself acts
as a template to form an RNA molecule of
the original sequence. Since each template
molecule can produce many copies of the
complementary strand, these reactions can
result in the amplification of the original
sequence.
original
RNA
A
G
G
U
C
C
A
U
C
ORIGINAL SEQUENCE
SERVES AS A TEMPLATE
TO PRODUCE THE
COMPLEMENTARY SEQUENCE
A
complementary
RNA
U
G
C
G
U
C
C
C
A
G
G
A
U
C
A
G
G
U
COMPLEMENTARY
SEQUENCE SERVES AS
A TEMPLATE TO PRODUCE
THE ORIGINAL SEQUENCE
A
U
G
C
G
U
C
C
A
C
A
G
G
U
255
RNA and the Origins of Life
Table 7–4 Biochemical Reactions that Can Be Catalyzed by
Ribozymes
Activity
Ribozymes
Peptide bond formation in protein
synthesis
ribosomal RNA
DNA ligation
in vitro selected RNA
RNA splicing
self-splicing RNAs, small nuclear RNAs
RNA polymerization
in vitro selected RNA
RNA phosphorylation
in vitro selected RNA
RNA aminoacylation
in vitro selected RNA
RNA alkylation
in vitro selected RNA
C–C bond rotation (isomerization)
in vitro selected RNA
5′
ribozyme
3′
5′
+
3′
substrate
RNA
BASE-PAIRING BETWEEN
RIBOZYME AND SUBSTRATE
5′
5′
fundamental steps in the expression of genetic information—especially
those steps where RNA molecules themselves are spliced or translated
into protein.
RNA, therefore, has all the properties required of a molecule that could
catalyze its own synthesis (Figure 7–47). Although self-replicating systems of RNA molecules have not been found in nature, scientists appear
to be well on the way to constructing them in the laboratory. Although
this demonstration would not prove that self-replicating RNA molecules
were essential to the origin of life on Earth, it would establish that such
a scenario is possible.
3′
3′
SUBSTRATE CLEAVAGE
5′
5′
3′
3′
PRODUCT RELEASE
RNA Is Thought to Predate DNA in Evolution
The first cells on Earth would presumably have been much less complex and less efficient in reproducing themselves than even the simplest
present-day cells. They would have consisted of little more than a simple
membrane enclosing a set of self-replicating molecules and a few other
components required to provide the materials and energy for this autocatalytic replication. If the evolutionary role for RNA proposed above is
correct, these earliest cells would also have differed fundamentally from
the cells we know today in having their hereditary information stored in
RNA rather than DNA.
Evidence that RNA arose before DNA in evolution can be found in the
chemical differences between them. Ribose (see Figure 7–3A), like
catalysis
Figure 7–47 Could an RNA molecule catalyze its
own synthesis? This hypothetical process would
require that the RNA catalyze both steps shown in
Figure 7–45. The red rays represent the active site
of this ribozyme.
+
ribozyme
cleaved
RNA
Figure 7–46 A ribozyme is an RNA
molecule that possesses catalytic activity.
The RNA molecule shown catalyzes the
cleavage of a second RNA at a specific
site. Similar ribozymes are found embedded
in large RNA genomes—called viroids—
that infect plants, where the cleavage
reaction is one step in the replication
of the viroid. (Adapted from T.R. Cech and
ECB4 e7.44/7.46
O.C. Uhlenbeck,
Nature 372:39–40, 1994.
With permission from Macmillan
Publishers Ltd.)
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Chapter 7
From DNA to Protein: How Cells Read the Genome
RNA-based systems
RNA
EVOLUTION OF RNAs THAT
CAN DIRECT PROTEIN SYNTHESIS
RNA- and protein-based systems
protein
RNA
EVOLUTION OF NEW ENZYMES
THAT SYNTHESIZE DNA AND
MAKE RNA COPIES FROM IT
present-day cells
DNA
RNA
protein
Figure 7–48 RNA may have preceded
DNA and proteins in evolution. According
to this hypothesis, RNA molecules provided
genetic, structural, and catalytic functions in
ECB4
e7.46/7.48
the earliest
cells.
DNA is now the repository
of genetic information, and proteins carry
out almost all catalysis in cells. RNA now
functions mainly as a go-between in protein
synthesis, while remaining a catalyst for
a few crucial reactions (including protein
synthesis).
Question 7–6
Discuss the following: “During the
evolution of life on Earth, RNA lost
its glorious position as the first selfreplicating catalyst. Its role now is as
a mere messenger in the information
flow from DNA to protein.”
glucose and other simple carbohydrates, is readily formed from formaldehyde (HCHO), which is one of the principal products of experiments
simulating conditions on the primitive Earth. The sugar deoxyribose is
harder to make, and in present-day cells it is produced from ribose in
a reaction catalyzed by a protein enzyme, suggesting that ribose predates deoxyribose in cells. Presumably, DNA appeared on the scene after
RNA, and then proved more suited than RNA as a permanent repository
of genetic information. In particular, the deoxyribose in its sugar–phosphate backbone makes chains of DNA chemically much more stable than
chains of RNA, so that greater lengths of DNA can be maintained without
breakage.
The other differences between RNA and DNA—the double-helical structure of DNA and the use of thymine rather than uracil—further enhance
DNA stability by making the molecule easier to repair. We saw in Chapter
6 that a damaged nucleotide on one strand of the double helix can be
repaired by using the other strand as a template. Furthermore, deamination, one of the most common unwanted chemical changes occurring in
polynucleotides, is easier to detect and repair in DNA than in RNA (see
Figure 6–23). This is because the product of the deamination of cytosine
is, by chance, uracil, which already exists in RNA, so that such damage
would be impossible for repair enzymes to detect in an RNA molecule.
However, in DNA, which has thymine rather than uracil, any uracil produced by the accidental deamination of cytosine is easily detected and
repaired.
Taken together, the evidence we have discussed supports the idea that
RNA—with its ability to provide genetic, structural, and catalytic functions—preceded DNA in evolution. As cells more closely resembling
present-day cells appeared, it is believed that many of the functions originally performed by RNA were taken over by DNA and proteins: DNA
took over the primary genetic function, and proteins became the major
catalysts, while RNA remained primarily as the intermediary connecting
the two (Figure 7–48). With the advent of DNA, cells were able to become
more complex, for they could then carry and transmit more genetic
information than could be stably maintained by RNA alone. Because of
the greater chemical complexity of proteins and the variety of chemical reactions they can catalyze, the shift (albeit incomplete) from RNA
to proteins also provided a much richer source of structural components
and enzymes. This enabled cells to evolve the great diversity of structure
and function that we see in life today.
Essential Concepts
•
The flow of genetic information in all living cells is DNA → RNA →
protein. The conversion of the genetic instructions in DNA into RNAs
and proteins is termed gene expression.
•
To express the genetic information carried in DNA, the nucleotide
sequence of a gene is first transcribed into RNA. Transcription is
catalyzed by the enzyme RNA polymerase, which uses nucleotide
sequences in the DNA molecule to determine which strand to use as
a template, and where to start and stop transcribing.
•
RNA differs in several respects from DNA. It contains the sugar ribose
instead of deoxyribose and the base uracil (U) instead of thymine (T).
RNAs in cells are synthesized as single-stranded molecules, which
often fold up into complex three-dimensional shapes.
•
Cells make several functional types of RNAs, including messenger
RNAs (mRNAs), which carry the instructions for making proteins;
ribosomal RNAs (rRNAs), which are the crucial components of
Essential Concepts
ribosomes; and transfer RNAs (tRNAs), which act as adaptor molecules in protein synthesis.
•
To begin transcription, RNA polymerase binds to specific DNA sites
called promoters that lie immediately upstream of genes. To initiate
transcription, eukaryotic RNA polymerases require the assembly of
a complex of general transcription factors at the promoter, whereas
bacterial RNA polymerase requires only an additional subunit, called
sigma factor.
•
Most protein-coding genes in eukaryotic cells are composed of a
number of coding regions, called exons, interspersed with larger
noncoding regions, called introns. When a eukaryotic gene is transcribed from DNA into RNA, both the exons and introns are copied.
•
Introns are removed from the RNA transcripts in the nucleus by RNA
splicing, a reaction catalyzed by small ribonucleoprotein complexes
known as snRNPs. Splicing removes the introns from the RNA and
joins together the exons—often in a variety of combinations, allowing
multiple proteins to be produced from the same gene.
•
Eukaryotic pre-mRNAs go through several additional RNA processing steps before they leave the nucleus as mRNAs, including 5′ RNA
capping and 3′ polyadenylation. These reactions, along with splicing,
take place as the pre-mRNA is being transcribed.
•
Translation of the nucleotide sequence of an mRNA into a protein
takes place in the cytoplasm on large ribonucleoprotein assemblies
called ribosomes. As the mRNA moves through the ribosome, its
message is translated into protein.
•
The nucleotide sequence in mRNA is read in sets of three nucleotides
called codons; each codon corresponds to one amino acid.
•
The correspondence between amino acids and codons is specified
by the genetic code. The possible combinations of the 4 different
nucleotides in RNA give 64 different codons in the genetic code. Most
amino acids are specified by more than one codon.
•
tRNAs act as adaptor molecules in protein synthesis. Enzymes called
aminoacyl-tRNA synthetases covalently link amino acids to their
appropriate tRNAs. Each tRNA contains a sequence of three nucleotides, the anticodon, which recognizes a codon in an mRNA through
complementary base-pairing.
•
Protein synthesis begins when a ribosome assembles at an initiation codon (AUG) in an mRNA molecule, a process that depends on
proteins called translation initiation factors. The completed protein
chain is released from the ribosome when a stop codon (UAA, UAG,
or UGA) in the mRNA is reached.
•
The stepwise linking of amino acids into a polypeptide chain is catalyzed by an rRNA molecule in the large ribosomal subunit, which thus
acts as a ribozyme.
•
The concentration of a protein in a cell depends on the rate at
which the mRNA and protein are synthesized and degraded. Protein
degradation in the cytosol and nucleus occurs inside large protein
complexes called proteasomes.
•
From our knowledge of present-day organisms and the molecules
they contain, it seems likely that life on Earth began with the evolution of RNA molecules that could catalyze their own replication.
•
It has been proposed that RNA served as both the genome and the
catalysts in the first cells, before DNA replaced RNA as a more stable
molecule for storing genetic information, and proteins replaced RNAs
as the major catalytic and structural components. RNA catalysts in
modern cells are thought to provide a glimpse into an ancient, RNAbased world.
257
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Chapter 7
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Key terms
alternative splicing
messenger RNA (mRNA)RNA polymerase
aminoacyl-tRNA synthetase
polyadenylationRNA processing
anticodon
promoterRNA splicing
codon
proteaseRNA transcript
exon
proteasomeRNA world
gene
reading frame
small nuclear RNA (snRNA)
gene expression
ribosomal RNA (rRNA)
spliceosome
general transcription factors
ribosome
transcription
genetic code
ribozyme
transfer RNA (tRNA)
initiator tRNARNA
translation
intronRNA capping
translation initiation factor
Questions
Question 7–7
Question 7–9
Which of the following statements are correct? Explain your
answers.
Use the genetic code shown in Figure 7–25 to identify which
of the following nucleotide sequences would code for the
polypeptide sequence arginine-glycine-aspartate:
A. An individual ribosome can make only one type of
protein.
1. 5′-AGA-GGA-GAU-3′
B. All mRNAs fold into particular three-dimensional
structures that are required for their translation.
2. 5′-ACA-CCC-ACU-3′
C.The large and small subunits of an individual ribosome
always stay together and never exchange partners.
4. 5′-CGG-GGU-GAC-3′
D.Ribosomes are cytoplasmic organelles that are
encapsulated by a single membrane.
E. Because the two strands of DNA are complementary,
the mRNA of a given gene can be synthesized using either
strand as a template.
F. An mRNA may contain the sequence
ATTGACCCCGGTCAA.
G.The amount of a protein present in a cell depends on
its rate of synthesis, its catalytic activity, and its rate of
degradation.
Question 7–8
The Lacheinmal protein is a hypothetical protein that causes
people to smile more often. It is inactive in many chronically
unhappy people. The mRNA isolated from a number of
different unhappy individuals in the same family was found
to lack an internal stretch of 173 nucleotides that is present
in the Lacheinmal mRNA isolated from happy members of
the same family. The DNA sequences of the Lacheinmal
genes from the happy and unhappy family members were
determined and compared. They differed by a single
nucleotide substitution, which lay in an intron. What can you
say about the molecular basis of unhappiness in this family?
(Hints: [1] Can you hypothesize a molecular mechanism by
which a single nucleotide substitution in a gene could cause
the observed deletion in the mRNA? Note that the deletion
is internal to the mRNA. [2] Assuming the 173-base-pair
deletion removes coding sequences from the Lacheinmal
mRNA, how would the Lacheinmal protein differ between
the happy and unhappy people?)
3. 5′-GGG-AAA-UUU-3′
Question 7–10
“The bonds that form between the anticodon of a tRNA
molecule and the three nucleotides of a codon in mRNA are
_____.” Complete this sentence with each of the following
options and explain why each of the resulting statements is
correct or incorrect.
A. Covalent bonds formed by GTP hydrolysis
B.Hydrogen bonds that form when the tRNA is at the
A site
C. Broken by the translocation of the ribosome along the
mRNA
Question 7–11
List the ordinary, dictionary definitions of the terms
replication, transcription, and translation. By their side, list
the special meaning each term has when applied to the
living cell.
Question 7–12
In an alien world, the genetic code is written in pairs of
nucleotides. How many amino acids could such a code
specify? In a different world, a triplet code is used, but the
sequence of nucleotides is not important; it only matters
which nucleotides are present. How many amino acids could
this code specify? Would you expect to encounter any
problems translating these codes?
Chapter 7 End-of-Chapter Questions
Question 7–13
Question 7–17
One remarkable feature of the genetic code is that amino
acids with similar chemical properties often have similar
codons. Thus codons with U or C as the second nucleotide
tend to specify hydrophobic amino acids. Can you suggest
a possible explanation for this phenomenon in terms of the
early evolution of the protein-synthesis machinery?
Which of the following types of mutations would be
predicted to harm an organism? Explain your answers.
Question 7–14
C. Deletion of three consecutive nucleotides in the middle
of the coding sequence.
A mutation in DNA generates a UGA stop codon in the
middle of the mRNA coding for a particular protein.
A second mutation in the cell’s DNA leads to a single
nucleotide change in a tRNA that allows the correct
translation of the protein; that is, the second mutation
“suppresses” the defect caused by the first. The altered
tRNA translates the UGA as tryptophan. What nucleotide
change has probably occurred in the mutant tRNA
molecule? What consequences would the presence of such
a mutant tRNA have for the translation of the normal genes
in this cell?
Question 7–15
The charging of a tRNA with an amino acid can be
represented by the following equation:
amino acid + tRNA + ATP → aminoacyl-tRNA + AMP + PPi
where PPi is pyrophosphate (see Figure 3–40). In the
aminoacyl-tRNA, the amino acid and tRNA are linked with
a high-energy covalent bond; a large portion of the energy
derived from the hydrolysis of ATP is thus stored in this
bond and is available to drive peptide bond formation at the
later stages of protein synthesis. The free-energy change of
the charging reaction shown in the equation is close to zero
and therefore would not be expected to favor attachment
of the amino acid to tRNA. Can you suggest a further step
that could drive the reaction to completion?
Question 7–16
A.The average molecular weight of a protein in the cell is
about 30,000 daltons. A few proteins, however, are much
larger. The largest known polypeptide chain made by any
cell is a protein called titin (made by mammalian muscle
cells), and it has a molecular weight of 3,000,000 daltons.
Estimate how long it will take a muscle cell to translate
an mRNA coding for titin (assume the average molecular
weight of an amino acid to be 120, and a translation rate of
two amino acids per second for eukaryotic cells).
B.Protein synthesis is very accurate: for every 10,000
amino acids joined together, only one mistake is made.
What is the fraction of average-sized protein molecules and
of titin molecules that are synthesized without any errors?
(Hint: the probability P of obtaining an error-free protein is
given by P = (1 – E)n, where E is the error frequency and n
the number of amino acids.)
C.The molecular weight of all eukaryotic ribosomal
proteins combined is about 2.5 × 106 daltons. Would it be
advantageous to synthesize them as a single protein?
D.Transcription occurs at a rate of about 30 nucleotides
per second. Is it possible to calculate the time required to
synthesize a titin mRNA from the information given here?
259
A.Insertion of a single nucleotide near the end of the
coding sequence.
B.Removal of a single nucleotide near the beginning of the
coding sequence.
D. Deletion of four consecutive nucleotides in the middle of
the coding sequence.
E.Substitution of one nucleotide for another in the middle
of the coding sequence.
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chapter EIGHT
8
Control of Gene Expression
An organism’s DNA encodes all of the RNA and protein molecules that are
needed to make its cells. Yet a complete description of the DNA sequence
of an organism—be it the few million nucleotides of a bacterium or the
few billion nucleotides in each human cell—does not enable us to reconstruct that organism any more than a list of all the English words in a
dictionary enables us to reconstruct a play by Shakespeare. We need to
know how the elements in the DNA sequence or the words on a list work
together to make the masterpiece.
For cells, the question involves gene expression. Even the simplest singlecelled bacterium can use its genes selectively—for example, switching
genes on and off to make the enzymes needed to digest whatever food
sources are available. In multicellular plants and animals, however, gene
expression is under much more elaborate control. Over the course of
embryonic development, a fertilized egg cell gives rise to many cell types
that differ dramatically in both structure and function. The differences
between an information-processing nerve cell and an infection-fighting
white blood cell, for example, are so extreme that it is difficult to imagine
that the two cells contain the same DNA (Figure 8–1). For this reason,
and because cells in an adult organism rarely lose their distinctive characteristics, biologists originally suspected that certain genes might be
selectively lost when a cell becomes specialized. We now know, however, that nearly all the cells of a multicellular organism contain the
same genome. Cell differentiation is instead achieved by changes in gene
expression.
In mammals, hundreds of different cell types carry out a range of specialized functions that depend upon genes that are switched on in that
An overview of gene
expression
how transcriptional
switches work
the molecular
mechanisms that create
specialized cell types
post-transcriptional
controls
262
Chapter 8
Control of Gene Expression
Figure 8–1 A neuron and a liver cell share the same genome.
The long branches of this neuron from the retina enable it to receive
electrical signals from many other neurons and carry them to many
neighboring neurons. The liver cell, which is drawn to the same scale,
is involved in many metabolic processes, including digestion and the
detoxification of alcohol and other drugs. Both of these mammalian
cells contain the same genome, but they express many different RNAs
and proteins. (Neuron adapted from S. Ramón y Cajal, Histologie
du Système Nerveux de l’Homme et de Vertébrés, 1909–1911. Paris:
Maloine; reprinted, Madrid: C.S.I.C., 1972.)
cell type but not in most others: for example, the β cells of the pancreas
make the protein hormone insulin, while the α cells of the pancreas make
the hormone glucagon; the B lymphocytes of the immune system make
antibodies, while developing red blood cells make the oxygen-transport
protein hemoglobin. The differences between a neuron, a white blood
cell, a pancreatic β cell, and a red blood cell depend upon the precise
control of gene expression. A typical differentiated cell expresses only
about half the genes in its total repertoire.
25 µm
In this chapter, we discuss the main ways in which gene expression is
regulated, with a focus on those genes that encode proteins as their
final product. Although some of these control mechanisms apply to both
eukaryotes and prokaryotes, eukaryotic cells—with their more complex
chromosomal structure—have some ways of controlling gene expression
that are not available to bacteria.
An Overview of Gene Expression
neuron
liver cell
Gene expression is a complex process by which cells selectively direct
the synthesis of the many thousands of proteins and RNAs encoded in
their genome. But how do cells coordinate and control such an intricate
process—and how does an individual cell specify which of its genes to
express? This decision is an especially important problem for animals
because, as they develop, their cells become highly specialized, ultimately producing an array of muscle, nerve, and blood cells, along with
the hundreds of other cell types seen in the adult. Such cell differentiation arises because cells make and accumulate different sets of RNA and
protein molecules: that is, they express different genes.
The Different Cell Types of a Multicellular Organism
Contain the Same DNA
ECB4 e8.01/8.01
The evidence that cells have the ability to change which genes they
express without altering the nucleotide sequence of their DNA comes
from experiments in which the genome from a differentiated cell is made
to direct the development of a complete organism. If the chromosomes of
the differentiated cell were altered irreversibly during development, they
would not be able to accomplish this feat.
Consider, for example, an experiment in which the nucleus is taken from
a skin cell in an adult frog and injected into a frog egg from which the
nucleus has been removed. In at least some cases, that doctored egg
will develop into a normal tadpole (Figure 8–2). Thus, the transplanted
skin-cell nucleus cannot have lost any critical DNA sequences. Nuclear
transplantation experiments carried out with differentiated cells taken
from adult mammals—including sheep, cows, pigs, goats, and mice—
have shown similar results. And in plants, individual cells removed from
a carrot, for example, can regenerate an entire adult carrot plant. These
experiments all show that the DNA in specialized cell types of multicellular organisms still contains the entire set of instructions needed to form
263
An Overview of Gene Expression
(A)
nucleus in
pipette
skin cells in
culture dish
adult frog
UV
tadpole
nucleus
injected
into egg
normal embryo
nucleus destroyed
by UV light
unfertilized egg
(B)
section
of carrot
proliferating
cell mass
separated
cells in rich
liquid
medium
(C)
single
cell
clone of
dividing
cells
young
embryo
young
plant
carrot
DONOR CELL
PLACED NEXT TO
ENUCLEATED EGG
cows
epithelial cells
from oviduct
ELECTRIC
PULSE CAUSES
DONOR CELL
TO FUSE WITH
ENUCLEATED
EGG CELL
meiotic
spindle
unfertilized
egg cell
CELL
DIVISION
reconstructed
embryo
zygote
embryo placed in
foster mother
calf
MEIOTIC SPINDLE
AND ASSOCIATED
CHROMOSOMES
REMOVED
Figure 8–2 Differentiated cells contain all the genetic instructions necessary to direct the formation of a
complete organism. (A) The nucleus of a skin cell from an adult frog transplanted into an egg whose nucleus has
been destroyed can give rise to an entire tadpole. The broken arrow indicates that to give the transplanted genome
time to adjust to an embryonic environment, a further transfer step is required in which one of the nuclei is taken
from the early embryo that begins to develop and is put back into a second enucleated egg. (B) In many types of
plants, differentiated cells retain the ability to “de-differentiate,” so that a single cell can proliferate to form a clone
of progeny cells that later give rise to an entire plant. (C) A nucleus removed from a differentiated cell from an adult
cow can be introduced into an enucleated egg from a different cow to give rise to a calf. Different calves produced
from the same differentiated cell donor are all clones of the donor and are therefore genetically identical.
(A, modified from J.B. Gurdon, Sci. Am. 219:24–35, 1968, with permission from the Estate of Bunji Tagawa.)
a whole organism. The various cell types of an organism therefore differ
not because they contain different genes, but because they express them
ECB4 e8.02/8.02
differently.
Different Cell Types Produce Different Sets of Proteins
The extent of the differences in gene expression between different cell
types may be roughly gauged by comparing the protein composition of
cells in liver, heart, brain, and so on. In the past, such analysis was performed by two-dimensional gel electrophoresis (see Panel 4–5, p. 167).
Nowadays, the total protein content of a cell can be rapidly analyzed by
264
Chapter 8
Control of Gene Expression
a method called mass spectrometry (see Figure 4–49). This technique is
much more sensitive than electrophoresis and it enables the detection of
even proteins that are produced in minor quantities.
Both techniques reveal that many proteins are common to all the cells of
a multicellular organism. These housekeeping proteins include, for example, the structural proteins of chromosomes, RNA polymerases, DNA
repair enzymes, ribosomal proteins, enzymes involved in glycolysis and
other basic metabolic processes, and many of the proteins that form the
cytoskeleton. In addition, each different cell type also produces specialized proteins that are responsible for the cell’s distinctive properties. In
mammals, for example, hemoglobin is made almost exclusively in developing red blood cells.
Gene expression can also be studied by cataloging a cell’s RNAs, including the mRNAs that encode protein. The most comprehensive methods for
such analyses involve determining the nucleotide sequence of every RNA
molecule made by the cell, an approach that can also reveal their relative abundance. Estimates of the number of different mRNA sequences in
human cells suggest that, at any one time, a typical differentiated human
cell expresses perhaps 5000–15,000 protein-coding genes from a total of
about 21,000. It is the expression of a different collection of genes in each
cell type that causes the large variations seen in the size, shape, behavior,
and function of differentiated cells.
A Cell Can Change the Expression of Its Genes in
Response to External Signals
The specialized cells in a multicellular organism are capable of altering their patterns of gene expression in response to extracellular cues.
For example, if a liver cell is exposed to the steroid hormone cortisol,
the production of several proteins is dramatically increased. Released
by the adrenal gland during periods of starvation, intense exercise, or
prolonged stress, cortisol signals liver cells to boost the production of
glucose from amino acids and other small molecules. The set of proteins whose production is induced by cortisol includes enzymes such
as tyrosine aminotransferase, which helps convert tyrosine to glucose.
When the hormone is no longer present, the production of these proteins
returns to its resting level.
Other cell types respond to cortisol differently. In fat cells, for example,
the production of tyrosine aminotransferase is reduced, while some other
cell types do not respond to cortisol at all. The fact that different cell
types often respond in different ways to the same extracellular signal
contributes to the specialization that gives each cell type its distinctive
character.
Gene Expression Can Be Regulated at Various Steps from
DNA to RNA to Protein
If differences among the various cell types of an organism depend on
the particular genes that the cells express, at what level is the control
of gene expression exercised? As we saw in the last chapter, there are
many steps in the pathway leading from DNA to protein, and all of them
can in principle be regulated. Thus a cell can control the proteins it contains by (1) controlling when and how often a given gene is transcribed,
(2) controlling how an RNA transcript is spliced or otherwise processed,
(3) selecting which mRNAs are exported from the nucleus to the cytosol,
(4) regulating how quickly certain mRNA molecules are degraded,
(5) selecting which mRNAs are translated into protein by ribosomes, or
How Transcriptional Switches Work
degraded mRNA
NUCLEUS
DNA
RNA
transcript
1
transcriptional
control
mRNA
2
RNA
processing
control
CYTOSOL
4
mRNA degradation
control
mRNA
5
3
translation
mRNA
control
transport
and
localization
control
protein
degradation
control
protein
6
degraded
protein
protein
7 activity
control
active
protein
inactive
protein
(6) regulating how rapidly specific proteins are destroyed after they have
been made; in addition, the activity of individual proteins can be further
regulated in a variety of ways. These steps are illustrated in Figure 8–3.
Gene expression can be regulated at each of these steps. For most genes,
however, the control of transcription (step number 1 in Figure 8–3) is
paramount. This makes sense because only transcriptional control can
ensure that no unnecessary intermediates are synthesized. So it is the
regulation of transcription—and the ECB4
DNAe8.03/8.03
and protein components that
determine which genes a cell transcribes into RNA—that we address first.
How Transcriptional Switches Work
Until 50 years ago, the idea that genes could be switched on and off was
revolutionary. This concept was a major advance, and it came originally
from studies of how E. coli bacteria adapt to changes in the composition
of their growth medium. Many of the same principles apply to eukaryotic
cells. However, the enormous complexity of gene regulation in higher
organisms, combined with the packaging of their DNA into chromatin,
creates special challenges and some novel opportunities for control—as
we will see. We begin with a discussion of the transcription regulators,
proteins that bind to DNA and control gene transcription.
Transcription Regulators Bind to Regulatory DNA
Sequences
Control of transcription is usually exerted at the step at which the process is initiated. In Chapter 7, we saw that the promoter region of a gene
binds the enzyme RNA polymerase and correctly orients the enzyme to
begin its task of making an RNA copy of the gene. The promoters of both
bacterial and eukaryotic genes include a transcription initiation site, where
RNA synthesis begins, plus a sequence of approximately 50 nucleotide
pairs that extends upstream from the initiation site (if one likens the
direction of transcription to the flow of a river). This upstream region
contains sites that are required for the RNA polymerase to recognize the
promoter, although they do not bind to RNA polymerase directly. Instead,
these sequences contain recognition sites for proteins that associate with
the active polymerase—sigma factor in bacteria (see Figure 7–9) or the
general transcription factors in eukaryotes (see Figure 7–12).
In addition to the promoter, nearly all genes, whether bacterial or eukaryotic, have regulatory DNA sequences that are used to switch the gene
on or off. Some regulatory DNA sequences are as short as 10 nucleotide
pairs and act as simple switches that respond to a single signal; such
simple regulatory switches predominate in bacteria. Other regulatory
DNA sequences, especially those in eukaryotes, are very long (sometimes spanning more than 10,000 nucleotide pairs) and act as molecular
265
Figure 8–3 Gene expression
in eukaryotic cells can be
controlled at various steps.
Examples of regulation at
each of these steps are
known, although for most
genes the main site of control
is step 1—transcription of a
DNA sequence into RNA.
266
Chapter 8
Control of Gene Expression
transcription regulator
base pair
sugar–phosphate
backbone
asparagine
CH2
major
groove
C
major groove
of DNA
2
Ser
2
3
3
Arg
CH3
minor
groove
Asn
1
H
N
1
(B)
O
(C)
N
H
H
H
H N
N H
H
N
A
N
N
O
Arg
(A)
T
N
O
H
minor groove
of DNA
Figure 8–4 A transcription regulator interacts with the major groove of a DNA double helix. (A) This regulator
recognizes DNA via three α helices, shown as numbered cylinders, which allow the protein to fit into the major
groove and form tight associations with the base pairs in a short stretch of DNA. This particular structural motif,
called a homeodomain, is found in many eukaryotic DNA-binding proteins (Movie 8.1). (B) Most of the contacts with
the DNA bases are made by helix 3 (red ), which is shown here end-on. The protein interacts with the edges of the
nucleotides without disrupting the hydrogen bonds that hold the base pairs together. (C) An asparagine residue
from helix 3 forms two hydrogen bonds with the adenine in an A-T base pair. The view is end-on looking down the
DNA double helix, and the protein contacts the base pair from the major groove side. For simplicity, only one amino
acid–base contact is shown; in reality, transcription regulators form hydrogen bonds (as shown here), ionic bonds,
and hydrophobic interactions with individual bases in the major groove. Typically, the protein–DNA interface would
consist of 10–20 such contacts, each involving a different amino acid and each contributing to the overall strength of
the protein–DNA interaction.
microprocessors,
integrating information from a variety of signals into a
ECB4
E8.04,05/8.04
command that dictates how often transcription of the gene is initiated.
Regulatory DNA sequences do not work by themselves. To have any
effect, these sequences must be recognized by proteins called transcription regulators. It is the binding of a transcription regulator to a
regulatory DNA sequence that acts as the switch to control transcription.
The simplest bacterium produces several hundred different transcription regulators, each of which recognizes a different DNA sequence and
thereby regulates a distinct set of genes. Humans make many more—several thousand—indicating the importance and complexity of this form of
gene regulation in the development and function of a complex organism.
Proteins that recognize a specific nucleotide sequence do so because
the surface of the protein fits tightly against the surface features of the
DNA double helix in that region. Because these surface features will vary
depending on the nucleotide sequence, different DNA-binding proteins
will recognize different nucleotide sequences. In most cases, the protein
inserts into the major groove of the DNA helix and makes a series of
intimate molecular contacts with the nucleotide pairs within the groove
(Figure 8–4). Although each individual contact is weak, the 10 to 20 contacts that are typically formed at the protein–DNA interface combine to
ensure that the interaction is both highly specific and very strong; indeed,
protein–DNA interactions are among the tightest and most specific
molecular interactions known in biology.
Many transcription regulators bind to the DNA helix as dimers (Figure
8–5). Such dimerization roughly doubles the area of contact with the
DNA, thereby greatly increasing the strength and specificity of the protein–DNA interaction.
How Transcriptional Switches Work
267
Transcriptional Switches Allow Cells to Respond to
Changes in Their Environment
The simplest and best understood examples of gene regulation occur in
bacteria and in the viruses that infect them. The genome of the bacterium
E. coli consists of a single circular DNA molecule of about 4.6 × 106 nucleotide pairs. This DNA encodes approximately 4300 proteins, although
only a fraction of these are made at any one time. Bacteria regulate the
expression of many of their genes according to the food sources that are
available in the environment. For example, in E. coli, five genes code for
enzymes that manufacture the amino acid tryptophan. These genes are
arranged in a cluster on the chromosome and are transcribed from a single promoter as one long mRNA molecule; such coordinately transcribed
clusters are called operons (Figure 8–6). Although operons are common
in bacteria, they are rare in eukaryotes, where genes are transcribed and
regulated individually (see Figure 7–2).
When tryptophan concentrations are low, the operon is transcribed;
the resulting mRNA is translated to produce a full set of biosynthetic
enzymes, which work in tandem to synthesize tryptophan. When tryptophan is abundant, however—for example, when the bacterium is in
the gut of a mammal that has just eaten a protein-rich meal—the amino
acid is imported into the cell and shuts down production of the enzymes,
which are no longer needed.
We now understand in considerable detail how this repression of the
tryptophan operon comes about. Within the operon’s promoter is a short
DNA sequence, called the operator (see Figure 8–6), that is recognized
by a transcription regulator. When this regulator binds to the operator, it
blocks access of RNA polymerase to the promoter, preventing transcription of the operon and production of the tryptophan-producing enzymes.
The transcription regulator is known as the tryptophan repressor, and it is
controlled in an ingenious way: the repressor can bind to DNA only if it
has also bound several molecules of tryptophan (Figure 8–7).
Figure 8–5 Many transcription regulators
bind to DNA as dimers. This transcription
regulator contains
leucine zipper motif,
ECB4 a
e8.05/8.05
which is formed by two α helices, each
contributed by a different protein subunit.
Leucine zipper proteins thus bind to DNA
as dimers, gripping the double helix like a
clothespin on a clothesline (Movie 8.2).
The tryptophan repressor is an allosteric protein (see Figure 4–41): the
binding of tryptophan causes a subtle change in its three-dimensional
structure so that the protein can bind to the operator sequence. When
the concentration of free tryptophan in the bacterium drops, the repressor no longer binds to DNA, and the tryptophan operon is transcribed.
The repressor is thus a simple device that switches production of a set of
biosynthetic enzymes on and off according to the availability of the end
product of the pathway that the enzymes catalyze.
The tryptophan repressor protein itself is always present in the cell. The
gene that encodes it is continuously transcribed at a low level, so that a
small amount of the repressor protein is always being made. Thus the
bacterium can respond very rapidly to a rise in tryptophan concentration.
promoter
E
D
C
B
A
E. coli chromosome
operator
mRNA molecule
series of enzymes required for tryptophan biosynthesis
Figure 8–6 A cluster of bacterial genes
can be transcribed from a single
promoter. Each of these five genes encodes
a different enzyme; all of the enzymes
are needed to synthesize the amino acid
tryptophan. The genes are transcribed as a
single mRNA molecule, a feature that allows
their expression to be coordinated. Clusters
of genes transcribed as a single mRNA
molecule are common in bacteria. Each of
these clusters is called an operon because
its expression is controlled by a regulatory
DNA sequence called the operator (green),
situated within the promoter. The yellow
blocks in the promoter represent DNA
sequences that bind RNA polymerase.
268
Chapter 8
Control of Gene Expression
promoter sequences
start of transcription
DNA
_ 60
_ 35
operator
tryptophan
low
_10
+1
+20
tryptophan
high
inactive repressor
RNA polymerase
active repressor
tryptophan
mRNA
OPERON ON
OPERON OFF
Figure 8–7 Genes can be switched off by repressor proteins. If the concentration of tryptophan inside a
bacterium is low (left), RNA polymerase (blue) binds to the promoter and transcribes the five genes of the tryptophan
operon. However, if the concentration of tryptophan is high (right), the repressor protein (dark green) becomes active
and binds to the operator (light green), where it blocks the binding of RNA polymerase to the promoter. Whenever
the concentration of intracellular tryptophan drops, the repressor falls off the DNA, allowing the polymerase to
again transcribe the operon. The promoter contains two key blocks of DNA sequence information, the –35 and –10
regions, highlighted in yellow, which are recognized by RNA polymerase (see Figure 7–10). The complete operon is
shown in Figure 8–6.
Repressors Turn Genes Off and Activators Turn Them On
The tryptophan repressor, as its name suggests, is a transcriptional
repressor protein: in its active form, it switches genes off, or represses
them. Some bacterial transcription regulators do the opposite: they switch
genes on, or activate them. These transcriptional activator proteins
ECB4
e8.07/8.07
work on
promoters
that—in contrast to the promoter for the tryptophan
operon—are only marginally able to bind and position RNA polymerase
on their own. However, these poorly functioning promoters can be made
fully functional by activator proteins that bind nearby and contact the
RNA polymerase to help it initiate transcription (Figure 8–8).
Like the tryptophan repressor, activator proteins often have to interact
with a second molecule to be able to bind DNA. For example, the bacterial activator protein CAP has to bind cyclic AMP (cAMP) before it can
bind to DNA (see Figure 4–19). Genes activated by CAP are switched on
in response to an increase in intracellular cAMP concentration, which
rises when glucose, the bacterium’s preferred carbon source, is no longer
available; as a result, CAP drives the production of enzymes that allow
the bacterium to digest other sugars.
An Activator and a Repressor Control the Lac Operon
Figure 8–8 Genes can be switched on by
activator proteins. An activator protein
binds to a regulatory sequence on the DNA
and then interacts with the RNA polymerase
to help it initiate transcription. Without
the activator, the promoter fails to initiate
transcription efficiently. In bacteria, the
binding of the activator to DNA is often
controlled by the interaction of a metabolite
or other small molecule (red triangle) with
the activator protein. The Lac operon works
in this manner, as we discuss shortly.
In many instances, the activity of a single promoter is controlled by two
different transcription regulators. The Lac operon in E. coli, for example,
bound activator
protein
binding site
for activator
protein
RNA polymerase
mRNA
5′
3′
How Transcriptional Switches Work
is controlled by both the Lac repressor and the CAP activator that we
just discussed. The Lac operon encodes proteins required to import and
digest the disaccharide lactose. In the absence of glucose, the bacterium
makes cAMP, which activates CAP to switch on genes that allow the cell
to utilize alternative sources of carbon—including lactose. It would be
wasteful, however, for CAP to induce expression of the Lac operon if lactose itself were not present. Thus the Lac repressor shuts off the operon
in the absence of lactose. This arrangement enables the control region
of the Lac operon to integrate two different signals, so that the operon
is highly expressed only when two conditions are met: glucose must be
absent and lactose must be present (Figure 8–9). This genetic circuit thus
behaves much like a switch that carries out a logic operation in a computer. When lactose is present AND glucose is absent, the cell executes the
appropriate program—in this case, transcription of the genes that permit
the uptake and utilization of lactose.
The elegant logic of the Lac operon first attracted the attention of biologists more than 50 years ago. The molecular basis of the switch in E. coli
was uncovered by a combination of genetics and biochemistry, providing the first insight into how transcription is controlled. In a eukaryotic
cell, similar transcription regulatory devices are combined to generate
increasingly complex circuits, including those that enable a fertilized egg
to form the tissues and organs of a multicellular organism.
CAPbinding
site
RNApolymerasebinding site
(promoter)
start of transcription
LacZ gene
operator
_80
_40
1
40
80
nucleotide pairs
OPERON OFF
+ GLUCOSE
+ LACTOSE
repressor
OPERON OFF
+ GLUCOSE
_ LACTOSE
cyclic
AMP
CAP
repressor
_ GLUCOSE
_ LACTOSE
OPERON OFF
RNA polymerase
_ GLUCOSE
OPERON ON
+ LACTOSE
mRNA
Figure 8–9 The Lac operon is controlled by two transcription regulators,
the Lac repressor and CAP. When lactose is absent, the Lac repressor binds
to the Lac operator and shuts off expression of the operon. Addition of lactose
increases the intracellular concentration of a related compound, allolactose;
allolactose binds to the Lac repressor, causing it to undergo a conformational
change that releases its grip on the operator DNA (not shown). When glucose is
absent, cyclic AMP (red triangle) is produced by the cell, and CAP binds to DNA.
LacZ, the first gene of the operon, encodes the enzyme β-galactosidase, which
breaks down lactose to galactose and
glucose.
ECB4
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Question 8–1
Bacterial cells can take up the
amino acid tryptophan (Trp) from
their surroundings, or if there is an
insufficient external supply they can
synthesize tryptophan from other
small molecules. The Trp repressor is
a transcription regulator that shuts
off the transcription of genes that
code for the enzymes required for
the synthesis of tryptophan (see
Figure 8–7).
A.What would happen to the
regulation of the tryptophan operon
in cells that express a mutant form
of the tryptophan repressor that
(1) cannot bind to DNA, (2) cannot
bind tryptophan, or (3) binds
to DNA even in the absence of
tryptophan?
B.What would happen in
scenarios (1), (2), and (3) if the
cells, in addition, produced normal
tryptophan repressor protein from a
second, normal gene?
269
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Chapter 8
Control of Gene Expression
Question 8–2
Explain how DNA-binding proteins
can make sequence-specific contacts
to a double-stranded DNA molecule
without breaking the hydrogen
bonds that hold the bases together.
Indicate how, through such contacts,
a protein can distinguish a T-A from
a C-G pair. Indicate the parts of the
nucleotide base pairs that could
form noncovalent interactions—
hydrogen bonds, electrostatic
attractions, or hydrophobic
interactions (see Panel 2–7,
pp. 78–79)—with a DNA-binding
protein. The structures of all the
base pairs in DNA are given in
Figure 5–6.
Eukaryotic Transcription Regulators Control Gene
Expression from a Distance
Eukaryotes, too, use transcription regulators—both activators and
repressors—to regulate the expression of their genes. The DNA sites to
which eukaryotic gene activators bind are termed enhancers, because
their presence dramatically enhances the rate of transcription. It was
surprising to biologists when, in 1979, it was discovered that these activator proteins could enhance transcription even when they are bound
thousands of nucleotide pairs away from a gene’s promoter. They also
work when bound either upstream or downstream from the gene. These
observations raised several questions. How do enhancer sequences and
the proteins bound to them function over such long distances? How do
they communicate with the promoter?
Many models for this “action at a distance” have been proposed, but the
simplest of these seems to apply in most cases. The DNA between the
enhancer and the promoter loops out to allow eukaryotic activator proteins to influence directly events that take place at the promoter (Figure
8–10). The DNA thus acts as a tether, allowing a protein that is bound
to an enhancer—even one that is thousands of nucleotide pairs away—
to interact with the proteins in the vicinity of the promoter—including
RNA polymerase and the general transcription factors (see Figure 7–12).
Often, additional proteins serve to link the distantly bound transcription
regulators to these proteins at the promoter; the most important of these
regulators is a large complex of proteins known as Mediator (see Figure
8–10). One of the ways in which these proteins function is by aiding the
assembly of the general transcription factors and RNA polymerase to
form a large transcription complex at the promoter. Eukaryotic repressor
proteins do the opposite: they decrease transcription by preventing the
assembly of the same protein complex.
In addition to promoting—or repressing—the assembly of a transcription
initiation complex directly, eukaryotic transcription regulators have an
additional mechanism of action: they attract proteins that modify chromatin structure and thereby affect the accessibility of the promoter to the
general transcription factors and RNA polymerase, as we discuss next.
eukaryotic
activator protein
Figure 8–10 In eukaryotes, gene
activation can occur at a distance.
An activator protein bound to a distant
enhancer attracts RNA polymerase
and general transcription factors to the
promoter. Looping of the intervening DNA
permits contact between the activator and
the transcription initiation complex bound
to the promoter. In the case shown here,
a large protein complex called Mediator
serves as a go-between. The broken stretch
of DNA signifies that the length of DNA
between the enhancer and the start of
transcription varies, sometimes reaching
tens of thousands of nucleotide pairs in
length. The TATA box is a DNA recognition
sequence for the first general transcription
factor that binds to the promoter (see
Figure 7–12).
DNA
TATA box
BINDING OF
GENERAL TRANSCRIPTION
FACTORS, MEDIATOR, AND
RNA POLYMERASE
enhancer
(binding site for
activator protein)
activator protein
Mediator
general
transcription
factors
TRANSCRIPTION BEGINS
RNA polymerase
start of
transcription
How Transcriptional Switches Work
271
Eukaryotic Transcription Regulators Help Initiate
Transcription by Recruiting Chromatin-Modifying Proteins
Initiation of transcription in eukaryotic cells must also take into account
the packaging of DNA into chromosomes. As discussed in Chapter 5,
eukaryotic DNA is packed into nucleosomes, which, in turn, are folded
into higher-order structures. How do transcription regulators, general
transcription factors, and RNA polymerase gain access to such DNA?
Nucleosomes can inhibit the initiation of transcription if they are positioned over a promoter, because they physically block the assembly of
the general transcription factors or RNA polymerase on the promoter.
Such chromatin packaging may have evolved in part to prevent leaky
gene expression by blocking the initiation of transcription in the absence
of the proper activator proteins.
In eukaryotic cells, activator and repressor proteins exploit chromatin
structure to help turn genes on and off. As we saw in Chapter 5, chromatin structure can be altered by chromatin-remodeling complexes and by
enzymes that covalently modify the histone proteins that form the core of
the nucleosome (see Figures 5–26 and 5–27). Many gene activators take
advantage of these mechanisms by recruiting such chromatin-modifying
proteins to promoters. For example, the recruitment of histone acetyltransferases promotes the attachment of acetyl groups to selected lysines
in the tail of histone proteins. This modification alters chromatin structure, allowing greater accessibility to the underlying DNA; moreover, the
acetyl groups themselves attract proteins that promote transcription,
including some of the general transcription factors (Figure 8–11).
Likewise, gene repressor proteins can modify chromatin in ways that
reduce the efficiency of transcription initiation. For example, many repressors attract histone deacetylases—enzymes that remove the acetyl groups
from histone tails, thereby reversing the positive effects that acetylation
has on transcription initiation. Although some eukaryotic repressor proteins work on a gene-by-gene basis, others can orchestrate the formation
of large swathes of transcriptionally inactive chromatin containing many
histone
octamer
Question 8–3
Some transcription regulators bind
to DNA and cause the double helix
to bend at a sharp angle. Such
“bending proteins” can stimulate
the initiation of transcription
without contacting either the RNA
polymerase, any of the general
transcription factors, or any other
transcription regulators. Can you
devise a plausible explanation for
how these proteins might work
to modulate transcription? Draw
a diagram that illustrates your
explanation.
transcription regulator
DNA
TATA box
histone
acetyltransferase
chromatin-remodeling
complex
TATA box
remodeled chromatin
specific pattern of
histone acetylation
general transcription factors,
Mediator, and
RNA polymerase
TRANSCRIPTION INITIATION
Figure 8–11 Eukaryotic transcriptional
activators can recruit chromatinmodifying proteins to help initiate gene
transcription. On the right, chromatinremodeling complexes render the DNA
packaged in chromatin more accessible to
other proteins in the cell, including those
required for transcription initiation; notice,
for example, the increased exposure of the
TATA box. On the left, the recruitment of
histone-modifying enzymes such as histone
acetyltransferases adds acetyl groups to
specific histones, which can then serve as
binding sites for proteins that stimulate
transcription initiation (not shown).
272
Chapter 8
Control of Gene Expression
genes. As discussed in Chapter 5, these transcription-resistant regions of
DNA include the heterochromatin found in interphase chromosomes and
the inactive X chromosome in the cells of female mammals.
The Molecular Mechanisms That Create
Specialized Cell Types
All cells must be able to switch genes on and off in response to signals in
their environment. But the cells of multicellular organisms have evolved
this capacity to an extreme degree and in highly specialized ways to form
organized arrays of differentiated cell types. In particular, once a cell in a
multicellular organism becomes committed to differentiate into a specific
cell type, the choice of fate is generally maintained through subsequent
cell divisions. This means that the changes in gene expression, which are
often triggered by a transient signal, must be remembered by the cell. This
phenomenon of cell memory is a prerequisite for the creation of organized tissues and for the maintenance of stably differentiated cell types.
In contrast, the simplest changes in gene expression in both eukaryotes
and bacteria are often only transient; the tryptophan repressor, for example, switches off the tryptophan operon in bacteria only in the presence
of tryptophan; as soon as the amino acid is removed from the medium,
the genes switch back on, and the descendants of the cell will have no
memory that their ancestors had been exposed to tryptophan.
In this section, we discuss some of the special features of transcriptional
regulation that are found in multicellular organisms. Our focus will be
on how these mechanisms create and maintain the specialized cell types
that give a worm, a fly, or a human its distinctive characteristics.
Eukaryotic Genes Are Controlled by Combinations of
Transcription Regulators
Because eukaryotic transcription regulators can control transcription initiation when bound to DNA many base pairs away from the promoter, the
nucleotide sequences that control the expression of a gene can be spread
over long stretches of DNA. In animals and plants, it is not unusual to
find the regulatory DNA sequences of a gene dotted over tens of thousands of nucleotide pairs, although much of the intervening DNA serves
as “spacer” sequence and is not directly recognized by the transcription
regulators.
So far in this chapter, we have treated transcription regulators as though
each functions individually to turn a gene on or off. While this idea holds
true for many simple bacterial activators and repressors, most eukaryotic
transcription regulators work as part of a “committee” of regulatory proteins, all of which are necessary to express the gene in the right place, in
the right cell type, in response to the right conditions, at the right time,
and in the required amount.
The term combinatorial control refers to the way that groups of transcription regulators work together to determine the expression of a single
gene. We saw a simple example of such regulation by multiple regulators when we discussed the bacterial Lac operon (see Figure 8–9). In
eukaryotes, the regulatory inputs have been amplified, and a typical gene
is controlled by dozens of transcription regulators. These help assemble chromatin-remodeling complexes, histone-modifying enzymes,
RNA polymerase, and general transcription factors via the multiprotein
Mediator complex (Figure 8–12). In many cases, both repressors and
activators will be present in the same complex; how the cell integrates
the effects of all of these proteins to determine the final level of gene
The Molecular Mechanisms That Create Specialized Cell Types
regulatory DNA sequences
spacer DNA
general
transcription
factors
chromatinremodeling
complex
Mediator
transcription
regulators
histonemodifying
enzyme
upstream
TATA
box
start of
transcription
RNA polymerase
promoter
expression is only now beginning to be understood. An example of such
a complex regulatory system—one that participates in the development of a fruit fly from a fertilized egg—is described in How We Know,
pp. 274–275.
The Expression of Different Genes Can Be Coordinated by
a Single Protein
In addition to being able to switch individual genes on and off, all cells—
whether prokaryote or eukaryote—need to coordinate the expression of
different genes. When a eukaryotic cell receives a signal to divide, for
example, a number of hitherto unexpressed genes are turned on together
ECB4 E8.12/8.12
to set in motion the events that lead eventually to cell division (discussed
in Chapter 18). As discussed earlier, one way in which bacteria coordinate the expression of a set of genes is by having them clustered together
in an operon under the control of a single promoter (see Figure 8–6).
Such clustering is not seen in eukaryotic cells, where each gene is transcribed and regulated individually. So how do these cells coordinate gene
expression? In particular, given that a eukaryotic cell uses a committee
of transcription regulators to control each of its genes, how can it rapidly
and decisively switch whole groups of genes on or off?
The answer is that even though control of gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in
switching any particular gene on or off, simply by completing the combination needed to activate or repress that gene. This is like dialing in
the final number of a combination lock: the lock will spring open if the
other numbers have been previously entered. Just as the same number
can complete the combination for different locks, the same protein can
complete the combination for several different genes. As long as different genes contain regulatory DNA sequences that are recognized by the
same transcription regulator, they can be switched on or off together, as
a coordinated unit.
An example of such coordinated regulation in humans is seen with the
cortisol receptor protein. In order to bind to regulatory sites in DNA, this
Figure 8–12 Transcription regulators
work together as a “committee” to
control the expression of a eukaryotic
gene. Whereas the general transcription
factors that assemble at the promoter
are the same for all genes transcribed by
RNA polymerase (see Figure 7–12), the
transcription regulators and the locations
of their DNA binding sites relative to the
promoters are different for different genes.
These regulators, along with chromatinmodifying proteins, are assembled at the
promoter by the Mediator. The effects of
multiple transcription regulators combine
to determine the final rate of transcription
initiation.
273
274
How we Know
gene regulation—the story of eve
The ability to regulate gene expression is crucial to
the proper development of a multicellular organism
from a fertilized egg to a fertile adult. Beginning at the
earliest moments in development, a succession of transcriptional programs guides the differential expression
of genes that allows an animal to form a proper body
plan—helping to distinguish its back from its belly, and
its head from its tail. These programs ultimately direct
the correct placement of a wing or a leg, a mouth or an
anus, a neuron or a sex cell.
A central challenge in development, then, is to understand how an organism generates these patterns of
gene expression, which are laid down within hours of
fertilization. Among the most important genes involved
in these early stages of development are those that
encode transcription regulators. By interacting with different regulatory DNA sequences, these proteins instruct
every cell in the embryo to switch on the genes that are
appropriate for that cell at each time point during development. How can a protein binding to a piece of DNA
help direct the development of a complex multicellular
organism? To see how we can address that large question, we review the story of Eve.
Seeing Eve
Even-skipped—Eve, for short—is a gene whose expression plays an important part in the development of the
Drosophila embryo. If this gene is inactivated by mutation, many parts of the embryo fail to form and the fly
larva dies early in development. But Eve is not expressed
uniformly throughout the embryo. Instead, the Eve protein is produced in a striking series of seven neat stripes,
each of which occupies a very precise position along the
length of the embryo. These seven stripes correspond to
seven of the fourteen segments that define the body plan
of the fly—three for the head, three for the thorax, and
eight for the abdomen.
This pattern never varies: Eve can be found in the very
same places in every Drosophila embryo (see Figure
8–13B). How can the expression of a gene be regulated
with such spatial precision—such that one cell will produce a protein while a neighboring cell does not? To find
out, researchers took a trip upstream.
Dissecting the DNA
As we have seen in this chapter, regulatory DNA
sequences control which cells in an organism will
express a particular gene, and at what point during
development that gene will be turned on. In eukaryotes,
these regulatory sequences are frequently located
upstream of the gene itself. One way to locate a regulatory DNA sequence—and study how it operates—is
to remove a piece of DNA from the region upstream
of a gene of interest and insert that DNA upstream of
a reporter gene—one that encodes a protein with an
activity that is easy to monitor experimentally. If the
piece of DNA contains a regulatory sequence, it will
drive the expression of the reporter gene. When this
patchwork piece of DNA is subsequently introduced into
a cell or organism, the reporter gene will be expressed
in the same cells and tissues that normally express the
gene from which the regulatory sequence was derived
(see Figure 10–31).
By excising various segments of the DNA sequences
upstream of Eve, and coupling them to a reporter gene,
researchers found that the expression of the gene is
controlled by a series of seven regulatory modules—
each of which specifies a single stripe of Eve expression.
In this way, researchers identified, for example, a single segment of regulatory DNA that specifies stripe 2.
They could excise this regulatory segment, link it to a
reporter gene, and introduce the resulting DNA segment
into the fly. When they examined embryos that carried
this engineered DNA, they found that the reporter gene
is expressed in the precise position of stripe 2 (Figure
8–13). Similar experiments revealed the existence of six
other regulatory modules, one for each of the other Eve
stripes.
The next question is: How does each of these seven regulatory segments direct the formation of a single stripe
in a specific position? The answer, researchers found,
is that each segment contains a unique combination
of regulatory sequences that bind different combinations of transcription regulators. These regulators, like
Eve itself, are distributed in unique patterns within the
embryo—some toward the head, some toward the rear,
some in the middle.
The regulatory segment that defines stripe 2, for
example, contains regulatory DNA sequences for four
transcription regulators: two that activate Eve transcription and two that repress it (Figure 8–14). In the narrow
band of tissue that constitutes stripe 2, it just so happens
the repressor proteins are not present—so the Eve gene
is expressed; in the bands of tissue on either side of the
stripe, the repressors keep Eve quiet. And so a stripe is
formed.
The regulatory segments controlling the other stripes
are thought to function along similar lines; each regulatory segment reads “positional information” provided
The Molecular Mechanisms That Create Specialized Cell Types
stripe 2
regulatory
segment
NORMAL
DNA
(A)
Eve regulatory segments
start of
transcription
EXCISE
(C)
stripe 2
regulatory
segment
TATA
box
Eve gene
(B)
start of
transcription
INSERT
REPORTER
FUSION DNA
275
TATA
box
LacZ gene
(D)
Figure 8–13 An experimental approach that involves the use of a reporter gene reveals the modular construction
of the Eve gene regulatory region. (A) Expression of the Eve gene is controlled by a series of regulatory segments
(orange) that direct the production of Eve protein in stripes along the embryo. (B) Embryos stained with antibodies to
the Eve protein show the seven characteristic stripes of Eve expression. (C) In the laboratory, the regulatory segment that
directs the formation of stripe 2 can be excised from the DNA shown in part A and inserted upstream of the E. coli LacZ
gene, which encodes the enzyme β-galactosidase (see Figure 8–9). (D) When the engineered DNA containing the stripe
2 regulatory segment is introduced into the genome
a fly, the resulting embryo expresses β-galactosidase precisely
ECB4ofm7.55/8.13
in the position of the second Eve stripe. Enzyme activity is assayed by the addition of X-gal, a modified sugar that when
cleaved by β-galactosidase generates an insoluble blue product. (B and D, courtesy of Stephen Small and Michael
Levine.)
by some unique combination of transcription regulators in the embryo and expresses Eve on the basis of
this information. The entire regulatory region is strung
out over 20,000 nucleotide pairs of DNA and, altogether,
binds more than 20 transcription regulators. This large
regulatory region is built from a series of smaller regulatory segments, each of which consists of a unique
arrangement of regulatory DNA sequences recognized
by specific transcription regulators. In this way, the
Eve gene can respond to an enormous combination of
inputs.
The Eve protein is itself a transcription regulator, and
it—in combination with many other regulatory proteins—controls key events in the development of the fly.
This complex organization of a discrete number of regulatory elements begins to explain how the development
of an entire organism can be orchestrated by repeated
applications of a few basic principles.
transcriptional repressors
Giant
Krüppel
stripe 2
regulatory
DNA segment
Bicoid
Hunchback
transcriptional activators
Figure 8–14 The regulatory segment that specifies Eve stripe 2 contains binding sites for four different
transcription regulators. All four regulators are responsible for the proper expression of Eve in stripe 2. Flies that are
deficient in the two activators, called Bicoid and Hunchback, fail to form stripe 2 efficiently; in flies deficient in either of
the two repressors, called Giant and Krüppel,
stripe
2 expands and covers an abnormally broad region of the embryo.
ECB4
e8.16/8.14
As indicated in the diagram, in some cases the binding sites for the transcription regulators overlap, and the proteins
compete for binding to the DNA. For example, the binding of Bicoid and Krüppel to the site at the far right is thought to
be mutually exclusive. The regulatory segment is 480 base pairs in length.
276
Chapter 8
Control of Gene Expression
Figure 8–15 A single transcription
regulator can coordinate the expression
of many different genes. The action of
the cortisol receptor is illustrated. On the
left is a series of genes, each of which
has a different gene activator protein
bound to its respective regulatory DNA
sequences. However, these bound proteins
are not sufficient on their own to activate
transcription efficiently. On the right is
shown the effect of adding an additional
transcription regulator—the cortisol–
receptor complex—that can bind to the
same regulatory DNA sequence in each
gene. The activated cortisol receptor
completes the combination of transcription
regulators required for efficient initiation
of transcription, and the genes are now
switched on as a set.
inactive cortisol
receptor in
absence of
cortisol
cortisol
activated cortisol
receptor
gene 1
gene 1
regulatory sequences for
cortisol–receptor complex
gene 2
gene 2
gene 3
gene 3
GENES EXPRESSED AT LOW LEVEL
GENES EXPRESSED AT HIGH LEVEL
transcription regulator must first form a complex with a molecule of cortisol (see Table 16–1, p. 529). In response to cortisol, liver cells increase the
expression of many genes, one of which encodes the enzyme tyrosine
aminotransferase, as discussed earlier. All these genes are regulated by
the binding of the cortisol–receptor complex to a regulatory sequence in
the DNA of each gene. When the cortisol concentration decreases again,
the expression of all of these genes drops to its normal level. In this way,
a single transcription regulator can coordinate the expression of many
different genes (Figure 8–15).
ECB4 e8.17/8.15
Combinatorial Control Can Also Generate Different Cell
Types
The ability to switch many different genes on or off using a limited number
of transcription regulators is not only useful in the day-to-day regulation
of cell function. It is also one of the means by which eukaryotic cells
diversify into particular types of cells during embryonic development.
A striking example is the development of muscle cells. A mammalian
skeletal muscle cell is distinguished from other cells by the production
of a large number of characteristic proteins, such as the muscle-specific
forms of actin and myosin that make up the contractile apparatus (discussed in Chapter 17), as well as the receptor proteins and ion channel
proteins in the plasma membrane that make the muscle cell sensitive to
nerve stimulation. The genes encoding these muscle-specific proteins are
all switched on coordinately as the muscle cell differentiates. Studies of
developing muscle cells in culture have identified a small number of key
transcription regulators, expressed only in potential muscle cells, that
coordinate muscle-specific gene expression and are thus crucial for muscle-cell differentiation. This set of regulators activates the transcription
of the genes that code for muscle-specific proteins by binding to specific
DNA sequences present in their regulatory regions.
Some transcription regulators can even convert one specialized cell type
to another. For example, when the gene encoding the transcription regulator MyoD is artificially introduced into fibroblasts cultured from skin
The Molecular Mechanisms That Create Specialized Cell Types
277
Figure 8–16 A small number of
transcription regulators can convert
one differentiated cell type directly into
another. In this experiment, liver cells grown
in culture (A) were converted into neuronal
cells (B) via the artificial introduction of three
nerve-specific transcription regulators. The
cells are labeled with a fluorescent dye.
(From S. Marro et al., Cell Stem Cell 9:374–
378, 2011. With permission from Elsevier.)
(A)
(B)
50 µm
50 µm
connective tissue, the fibroblasts form musclelike cells. It appears that
the fibroblasts, which are derived from the same broad class of embryECB4 n8.100/8.16
onic cells as muscle cells, have already accumulated many of the other
necessary transcription regulators required for the combinatorial control
of the muscle-specific genes, and that addition of MyoD completes the
unique combination required to direct the cells to become muscle.
This type of reprogramming can produce even more dramatic effects. For
example, a set of nerve-specific transcription regulators, when artificially
expressed in cultured liver cells, can convert them into functional neurons (Figure 8–16). Such dramatic results suggest that it may someday
be possible to produce in the laboratory any cell type for which the correct combination of transcription regulators can be identified. How these
transcription regulators can then lead to the generation of different cell
types is illustrated schematically in Figure 8–17.
precursor cell
REGULATORY PROTEIN
1
cell division
1
REGULATORY
PROTEIN 2
REGULATORY
PROTEIN 2
REGULATORY
PROTEIN 3
cell type
A
3
2
cell type
B
cell type
C
1
1
2
REGULATORY
PROTEIN 3
2
3
cell type
D
1
cell type
E
2
REGULATORY
PROTEIN 3
1
3
cell type
F
1
REGULATORY
PROTEIN 3
2
cell type
G
1
2
3
cell type
H
Figure 8–17 Combinations of a few
transcription regulators can generate
many cell types during development. In
this simple scheme, a “decision” to make
a new transcription regulator (shown as a
numbered circle) is made after each cell
division. Repetition of this simple rule can
generate eight cell types (A through H),
using only three transcription regulators.
Each of these hypothetical cell types would
then express many different genes, as
dictated by the combination of transcription
regulators that each cell type produces.
278
Chapter 8
Control of Gene Expression
Figure 8–18 A combination of
transcription regulators can induce a
differentiated cell to de-differentiate
into a pluripotent cell. The artificial
expression of a set of four genes, each of
which encodes a transcription regulator, can
reprogram a fibroblast into a pluripotent
cell with ES cell-like properties. Like ES cells,
such iPS cells can proliferate indefinitely
in culture and can be stimulated by
appropriate extracellular signal molecules
to differentiate into almost any cell type in
the body.
GENES ENCODING THREE
TRANSCRIPTION REGULATORS
INTRODUCED INTO
FIBROBLAST NUCLEUS
CELLS ALLOWED
TO DIVIDE
oct4
IN CULTURE
Sox2
klf4
CELLS INDUCED
TO DIFFERENTIATE
IN CULTURE
muscle cell
neuron
fibroblast
iPS cell
fat cell
Specialized Cell Types Can Be Experimentally
ECB4 n8.101/8.18
Reprogrammed to Become Pluripotent Stem Cells
We have seen that, in some cases, one type of differentiated cell can be
experimentally converted into another type by the artificial expression of
specific transcription regulators (see Figure 8–16). Even more surprising,
transcription regulators can coax various differentiated cells to de-differentiate into pluripotent stem cells that are capable of giving rise to all
the specialized cell types in the body, much like the embryonic stem (ES)
cells discussed in Chapter 20 (see pp. 708–711).
Using a defined set of transcription regulators, cultured mouse fibroblasts
have been reprogrammed to become induced pluripotent stem (iPS)
cells—cells that look and behave like the pluripotent ES cells that are
derived from embryos (Figure 8–18). The approach was quickly adapted
to produce iPS cells from a variety of specialized cell types, including cells
taken from humans. Such human iPS cells can then be directed to generate a population of differentiated cells for use in the study or treatment of
disease, as we discuss in Chapter 20.
eye structure on leg
100 µm
Figure 8–19 Artificially induced
expression of the Drosophila Ey gene in
the precursor cells of the leg triggers the
misplaced development of an eye on a
fly’s leg. (Courtesy of Walter Gehring.)
ECB4 e8.23b/8.19
The Formation of an Entire Organ Can Be Triggered
by a Single Transcription Regulator
We have seen that a small number of transcription regulators can control
the expression of whole sets of genes and can even convert one cell type
into another. But an even more stunning example of the power of transcriptional control comes from studies of eye development in Drosophila.
In this case, a single “master” transcription regulator called Ey could be
used to trigger the formation of not just a single cell type but a whole
organ. In the laboratory, the Ey gene can be artificially expressed in fruit
fly embryos in cells that would normally give rise to a leg. When these
modified embryos develop into adult flies, some have an eye in the middle
of a leg (Figure 8–19).
How the Ey protein coordinates the specification of each type of cell found
in the eye—and directs their proper organization in three-dimensional
space—is an actively studied topic in developmental biology. In essence,
however, Ey functions like any other transcription regulator, controlling
the expression of multiple genes by binding to DNA sequences in their
regulatory regions. Some of the genes controlled by Ey encode additional
transcription regulators that, in turn, control the expression of other
genes. In this way, the action of a single transcription regulator can produce a cascade of regulators that, working in combination, lead to the
formation of an organized group of many different types of cells. One can
begin to imagine how, by repeated applications of this principle, a complex organism self-assembles, piece by piece.
The Molecular Mechanisms That Create Specialized Cell Types
279
Epigenetic Mechanisms Allow Differentiated Cells to
Maintain Their Identity
Once a cell has become differentiated into a particular cell type, it will
generally remain differentiated, and all its progeny cells will remain that
same cell type. Some highly specialized cells, including skeletal muscle
cells and neurons, never divide again once they have differentiated—that
is, they are terminally differentiated (as discussed in Chapter 18). But many
other differentiated cells—such as fibroblasts, smooth muscle cells, and
liver cells—will divide many times in the life of an individual. When they
do, these specialized cell types give rise only to cells like themselves:
smooth muscle cells do not give rise to liver cells, nor liver cells to
fibroblasts.
For a proliferating cell to maintain its identity—a property called cell
memory—the patterns of gene expression responsible for that identity
must be remembered and passed on to its daughter cells through all subsequent cell divisions. Thus, in the model illustrated in Figure 8–17, the
production of each transcription regulator, once begun, has to be continued in the daughter cells of each cell division. How is such perpetuation
accomplished?
Cells have several ways of ensuring that their daughters “remember”
what kind of cells they are. One of the simplest and most important is
through a positive feedback loop, where a master transcription regulator activates transcription of its own gene, in addition to that of other
cell-type–specific genes. Each time a cell divides the regulator is distributed to both daughter cells, where it continues to stimulate the positive
feedback loop. The continued stimulation ensures that the regulator will
continue to be produced in subsequent cell generations. The Ey protein
discussed earlier functions in such a positive feedback loop. Positive
feedback is crucial for establishing the “self-sustaining” circuits of gene
expression that allow a cell to commit to a particular fate—and then to
transmit that information to its progeny (Figure 8–20).
Although positive feedback loops are probably the most prevalent way of
ensuring that daughter cells remember what kind of cells they are meant
to be, there are other ways of reinforcing cell identity. One involves the
methylation of DNA. In vertebrate cells, DNA methylation occurs on certain cytosine bases (Figure 8–21). This covalent modification generally
progeny cells
A
CELL
MEMORY
A
A
GENE A CONTINUES
TO BE TRANSCRIBED
IN ABSENCE OF
INITIAL SIGNAL
gene A
A
A
CELL
MEMORY
A
A
A
transcriptional
factor, protein A,
is not made
because it is
normally required
for the transcription
of its own gene
TRANSIENT
SIGNAL
TURNS ON
EXPRESSION
OF GENE A
A
A
A
A
parent cell
Figure 8–20 A positive feedback
loop can create cell memory.
Protein A is a master transcription
regulator that activates the
transcription of its own gene—as
well as other cell-type-specific
genes (not shown). All of the
descendants of the original cell
will therefore “remember” that the
progenitor cell had experienced a
transient signal that initiated the
production of protein A.
280
Chapter 8
Control of Gene Expression
cytosine
H
H
H
N
5-methylcytosine
H
H
N
H 3C
5 4 3N
methylation
6 1 2
H
O
N
H
N
O
N
Figure 8–21 Formation of
5-methylcytosine occurs by methylation
of a cytosine base in the DNA double
helix. In vertebrates, this modification
is confined to selected cytosine (C)
nucleotides that
falle8.21/8.21
next to a guanine (G) in
ECB4
the sequence CG.
turns off genes by attracting proteins that bind to methylated cytosines
and block gene transcription. DNA methylation patterns are passed on
to progeny cells by the action of an enzyme that copies the methylation
pattern on the parent DNA strand to the daughter DNA strand as it is synthesized (Figure 8–22).
Another mechanism for inheriting gene expression patterns involves the
modification of histones. When a cell replicates its DNA, each daughter
double helix receives half of its parent’s histone proteins, which contain
the covalent modifications of the parent chromosome. Enzymes responsible for these modifications may bind to the parental histones and confer
the same modifications to the new histones nearby. This cycle of modification reestablishes the pattern of chromatin structure found in the
parent chromosome (Figure 8–23).
Because all of these cell-memory mechanisms transmit patterns of
gene expression from parent to daughter cell without altering the actual
nucleotide sequence of the DNA, they are considered to be forms of
epigenetic inheritance. Such epigenetic changes play an important part
in controlling patterns of gene expression, allowing transient signals
from the environment to be permanently recorded by our cells—a fact
that has important implications for understanding how cells operate and
how they malfunction in disease.
Post-Transcriptional Controls
We have seen that transcription regulators control gene expression
by promoting or hindering the transcription of specific genes. The vast
majority of genes in all organisms are regulated in this way. But many
additional points of control can come into play later in the pathway from
DNA to protein, giving cells a further opportunity to regulate the amount
or activity of the gene products that they make (see Figure 8–3). These
post-transcriptional controls, which operate after transcription has
begun, play a crucial part in regulating the expression of almost all genes.
We have already encountered a few examples of such post-transcriptional control. We have seen how alternative RNA splicing allows different
CH3
methylated
cytosine
unmethylated
cytosine
5′
C G
CH3
C G
3′
DNA
3′
G C
G C
5′
DNA
REPLICATION
5′
3′
C G
C G
G C
G C
3′
METHYLATION
OF NEWLY
SYNTHESIZED
STRAND
5′
CH3
5′
3′
C G
C G
G C
G C
3′
5′
H3C
not recognized
recognized by
by maintenance
maintenance
methyltransferase methyltransferase
new DNA
strands
CH3
H3C
5′
3′
C G
C G
G C
G C
H3C
3′
5′
5′
METHYLATION
OF NEWLY
SYNTHESIZED
STRAND
3′
C G
C G
G C
G C
3′
5′
H 3C
Figure 8–22 DNA methylation patterns can be faithfully inherited when a cell divides. An enzyme called a maintenance
methyltransferase guarantees that once a pattern of DNA methylation has been established, it is inherited by newly made DNA.
Immediately after DNA replication, each daughter double helix will contain one methylated DNA strand—inherited from the parent
double helix—and one unmethylated, newly synthesized strand. The maintenance methyltransferase interacts with these hybrid double
helices and methylates only those CG sequences that are base-paired with a CG sequence that is already methylated.
Post-Transcriptional Controls
parental nucleosomes with
modified histones
only half of the daughter
nucleosomes inherit the
modified parental histones
parental pattern of histone
modification reestablished
by enzymes that recognize
the same modifications they
catalyze
forms of a protein, encoded by the same gene, to be made in different
tissues (Figure 7–22). And we have discussed how various post-translational modifications of a protein can regulate its concentration and
activity (see Figure 4–43). In the remainder of this chapter, we consider
several other examples—some only recently discovered—of the many
ways in which cells can manipulate the expression of a gene after transcription has commenced.
Each mRNA Controls Its Own Degradation and Translation
ECB4 m5.32/8.23
The more time an mRNA persists in the cell before it is degraded, the
more protein it will produce. In bacteria, most mRNAs last only a few minutes before being destroyed. This instability allows a bacterium to adapt
quickly to environmental changes. Eukaryotic mRNAs are generally more
stable. The mRNA that encodes β-globin, for example, has a half-life of
more than 10 hours. Most eukaryotic mRNAs, however, have half-lives
of less than 30 minutes, and the most short-lived are those that encode
proteins whose concentrations need to change rapidly based on the cell’s
needs, such as transcription regulators. Whether bacterial or eukaryotic,
an mRNA’s lifetime is dictated by specific nucleotide sequences within
the untranslated regions that lie both upstream and downstream of the
protein-coding sequence. These sequences often harbor binding sites for
proteins that are involved in RNA degradation.
In addition to the nucleotide sequences that regulate its half-life, each
mRNA possesses sequences that help control how often or how efficiently
it will be translated into protein. These sequences control translation initiation. Although the details differ between eukaryotes and bacteria, the
general strategy is similar for both.
Bacterial mRNAs contain a short ribosome-binding sequence located
a few nucleotide pairs upstream of the AUG codon where translation
begins (see Figure 7–37). This binding sequence forms base pairs with the
RNA in the small ribosomal subunit, correctly positioning the initiating
AUG codon within the ribosome. Because this interaction is needed for
efficient translation initiation, it provides an ideal target for translational
control. By blocking—or exposing—the ribosome-binding sequence, the
bacterium can either inhibit—or promote—the translation of an mRNA
(Figure 8–24).
Eukaryotic mRNAs possess a 5′ cap that helps guide the ribosome to
the first AUG, the codon where translation will start (see Figure 7–36).
Eukaryotic repressor proteins can inhibit translation initiation by binding to specific nucleotide sequences in the 5′ untranslated region of the
mRNA, thereby preventing the ribosome from finding the first AUG—a
mechanism similar to that in bacteria. When conditions change, the cell
can inactivate the repressor to initiate translation of the mRNA.
281
Figure 8–23 Histone modifications
may be inherited by daughter
chromosomes. When a chromosome
is replicated, its resident histones are
distributed more or less randomly
to each of the two daughter DNA
double helices. Thus, each daughter
chromosome will inherit about half of its
parent’s collection of modified histones.
The remaining stretches of DNA receive
newly synthesized, not-yet-modified
histones. If the enzymes responsible for
each type of modification bind to the
specific modification they create, they can
catalyze the spread of this modification
on the new histones. This cycle of
modification and recognition can restore
the parental histone modification pattern
and, ultimately, allow the inheritance of
the parental chromatin structure. This
mechanism may apply to some but not all
types of histone modifications.
282
Chapter 8
Control of Gene Expression
5′
AUG
3′
mRNA
PROTEIN
MADE
5′
AUG
ribosome-binding site
NO PROTEIN
MADE
3′
INCREASED TEMPERATURE
EXPOSES RIBOSOME-BINDING SITE
translation repressor protein
5′
AUG
(A)
Figure 8–24 A bacterial gene’s expression
can be controlled by regulating
translation of its mRNA. (A) Sequencespecific RNA-binding proteins can repress
the translation of specific mRNAs by
keeping the ribosome from binding to the
ribosome-binding sequence (orange) in the
mRNA. Some ribosomal proteins exploit
this mechanism to inhibit the translation
of their own mRNA. In this way, “extra”
ribosomal proteins—those not incorporated
into ribosomes—serve as a signal to halt
their synthesis. (B) An mRNA from the
pathogen Listeria monocytogenes contains
a “thermosensor” RNA sequence that
controls the translation of a set of mRNAs
produced by virulence genes. At the warmer
temperature that the bacterium encounters
inside its human host, the thermosensor
sequence denatures, exposing the
ribosome-binding sequence, so the
virulence proteins are made.
3′
NO PROTEIN
MADE
5′
AUG
3′
PROTEIN
MADE
(B)
Regulatory RNAs Control the Expression of Thousands of
Genes
As we saw in Chapter 7, RNAs perform many critical tasks in cells. In
addition to the mRNAs, which code for proteins, noncoding RNAs have
various functions. It has long been known that some have key structural
and catalytic roles, particularly in protein synthesis by ribosomes (see
pp. 246–247). But a recent series of surprising discoveries has revealed
several new classes of noncoding RNAs and shown that these RNAs are
far more prevalent than previously suspected.
What, then, are all these newly discovered noncoding RNAs doing? Many
have unanticipated but important roles in regulating gene expression and
are therefore referred to as regulatory RNAs. There are at least three
major types of regulatory RNAs—microRNAs, small interfering RNAs, and
long noncoding RNAs. We discuss each one in turn.
MicroRNAs Direct the Destruction of Target mRNAs
ECB4 e8.25/8.24
MicroRNAs,
or miRNAs, are tiny RNA molecules that control gene
expression by base-pairing with specific mRNAs and reducing both
their stability and their translation into protein. In humans, miRNAs are
thought to regulate the expression of at least one-third of all proteincoding genes.
Like other noncoding RNAs, such as tRNA and rRNA, a precursor miRNA
transcript undergoes a special type of processing to yield the mature,
functional miRNA molecule, which is only about 22 nucleotides in length.
This small but mature miRNA is packaged with specialized proteins to
form an RNA-induced silencing complex (RISC), which patrols the cytoplasm in search of mRNAs that are complementary to the bound miRNA
molecule (Figure 8–25). Once a target mRNA forms base pairs with an
miRNA, it is either destroyed immediately by a nuclease present within
the RISC or its translation is blocked. In the latter case, the bound mRNA
molecule is delivered to a region of the cytoplasm where other nucleases
eventually degrade it. Destruction of the mRNA releases the RISC and
allows it to seek out additional mRNA targets. Thus, a single miRNA—as
part of a RISC—can eliminate one mRNA molecule after another, thereby
efficiently blocking production of the protein that the mRNAs encode.
Two features of miRNAs make them especially useful regulators of
gene expression. First, a single miRNA can inhibit the transcription of a
whole set of different mRNAs so long as all the mRNAs carry a common
sequence, usually located in either their 5′ or 3′ untranslated regions.
In humans, some individual miRNAs influence the transcription of hundreds of different mRNAs in this manner. Second, a gene that encodes an
miRNA occupies relatively little space in the genome compared with one
that encodes a transcription regulator. Indeed, their very small size is one
reason that miRNAs were discovered only recently. There are thought
Post-Transcriptional Controls
Figure 8–25 An miRNA targets a
complementary mRNA molecule for
destruction. Each precursor miRNA
transcript is processed to form a doublestranded intermediate, which is further
processed to form a mature, single-stranded
miRNA. This miRNA assembles with a set
of proteins into a complex called RISC,
which then searches for mRNAs that have
a nucleotide sequence complementary
to its bound miRNA. Depending on how
extensive the region of complementarity is,
the target mRNA is either rapidly degraded
by a nuclease within the RISC or transferred
to an area of the cytoplasm where other
cellular nucleases destroy it.
precursor
miRNA
AAAAA
PROCESSING AND
EXPORT TO CYTOPLASM
NUCLEUS
CYTOSOL
RISC
proteins
double-stranded
RNA intermediate
FORMATION OF RISC
single-stranded miRNA
3′
283
5′
SEARCH FOR COMPLEMENTARY
TARGET mRNA
extensive match
mRNA
AAAAA
mRNA
RAPIDLY
DEGRADED
less extensive match
mRNA
RISC
released
AAAAA
mRNA TRANSLATION REDUCED;
mRNA SEQUESTERED AND
EVENTUALLY DEGRADED
foreign double-stranded RNA
CLEAVAGE BY DICER
to be roughly 500 different miRNAs encoded by the human genome.
Although we are only beginning to understand the full impact of these
miRNAs, it is clear that they play a critical part in regulating gene expression and thereby influence many cell functions.
Small Interfering RNAs Are Produced From DoubleStranded, Foreign RNAs to Protect Cells From Infections
foreign
double-stranded
siRNAs
RISC
proteins
single-stranded siRNA
ECB4 e8.26/8.25
Some of the same components
that process and package miRNAs also
play another crucial part in the life of a cell: they serve as a powerful
cell defense mechanism. In this case, the system is used to eliminate
“foreign” RNA molecules—in particular, the double-stranded RNAs produced by many viruses and transposable genetic elements (discussed in
Chapter 9). The process is called RNA interference (RNAi).
In the first step of RNAi, the double-stranded, foreign RNAs are cut into
short fragments (approximately 22 nucleotide pairs in length) by a protein called Dicer—the same protein used to generate the double-stranded
RNA intermediate in miRNA production (see Figure 8–25). The resulting double-stranded RNA fragments, called small interfering RNAs
(siRNAs), are then taken up by the same RISCs that carry miRNAs. The
RISC discards one strand of the siRNA duplex and uses the remaining
single-stranded RNA to seek and destroy complementary foreign RNA
molecules (Figure 8–26). In this way, the infected cell turns the foreign
RNA back on itself.
RNAi operates in a wide variety of organisms, including single-celled
fungi, plants, and worms, indicating that it is an evolutionarily ancient
defense mechanism. In some organisms, including plants, the RNAi
defense response can spread from tissue to tissue, allowing the entire
organism to become resistant to a virus after only a few of its cells
FORMATION OF RISC
SEARCH FOR
COMPLEMENTARY
RNA
siRNA
foreign RNA
FOREIGN RNA
DEGRADED
RISC
released
Figure 8–26 siRNAs are produced from
double-stranded, foreign RNAs in the
process of RNA interference. Doublestranded RNAs from a virus or transposable
genetic element are first cleaved by a
ECB4 e8.27/8.26
nuclease called Dicer.
The resulting doublestranded fragments are incorporated into
RISCs, which discard one strand of the
foreign RNA duplex and use the other
strand to locate and destroy foreign RNAs
with a complementary sequence.
284
Chapter 8
Control of Gene Expression
have been infected. In this sense, RNAi resembles certain aspects of the
adaptive immune responses of vertebrates; in both cases, an invading
pathogen elicits the production of molecules—either siRNAs or antibodies—that are custom-made to inactivate the specific invader and thereby
protect the host.
Thousands of Long Noncoding RNAs May Also
Regulate Mammalian Gene Activity
At the other end of the size spectrum are the long noncoding RNAs, a
class of RNA molecules that are more than 200 nucleotides in length.
There are thought to be upwards of 8000 of these RNAs encoded in the
human and mouse genomes. Yet, with few exceptions, their roles in the
biology of the organism are not entirely clear.
One of the best understood of the long noncoding RNAs is Xist. This enormous RNA molecule, some 17,000 nucleotides long, is a key player in X
inactivation—the process by which one of the two X chromosomes in the
cells of female mammals is permanently silenced (see Figure 5–30). Early
in development, Xist is produced by only one of the X chromosomes in
each female nucleus. The transcript then “sticks around,” coating the
chromosome and presumably attracting the enzymes and chromatinremodeling complexes that promote the formation of highly condensed
heterochromatin. Other long noncoding RNAs may promote the silencing
of specific genes in a similar manner.
Some long noncoding RNAs arise from protein-coding regions of the
genome, but are transcribed from the “wrong” DNA strand. Some of these
antisense transcripts are known to bind to the mRNAs produced from that
DNA segment, regulating their translation and stability—in some cases
by producing siRNAs (see Figure 8–26).
Regardless of how the various long noncoding RNAs operate—or what
exactly they do—the discovery of this large class of RNAs reinforces the
idea that a eukaryotic genome is densely packed with information that
provides not only an inventory of the molecules and structures every cell
must make, but a set of instructions for how and when to assemble these
parts to guide the growth and development of a complete organism.
Essential Concepts
•
A typical eukaryotic cell expresses only a fraction of its genes, and
the distinct types of cells in multicellular organisms arise because
different sets of genes are expressed as cells differentiate.
•
In principle, gene expression can be controlled at any of the steps
between a gene and its ultimate functional product. For the majority
of genes, however, the initiation of transcription is the most important point of control.
•
The transcription of individual genes is switched on and off in cells by
transcription regulator proteins, which bind to short stretches of DNA
called regulatory DNA sequences.
•
In bacteria, transcription regulators usually bind to regulatory DNA
sequences close to where RNA polymerase binds. This binding can
either activate or repress transcription of the gene. In eukaryotes,
regulatory DNA sequences are often separated from the promoter by
many thousands of nucleotide pairs.
•
Eukaryotic transcription regulators act in two main ways: (1) they can
directly affect the assembly process that requires RNA polymerase
Essential Concepts
and the general transcription factors at the promoter, and (2) they
can locally modify the chromatin structure of promoter regions.
•
In eukaryotes, the expression of a gene is generally controlled by a
combination of different transcription regulator proteins.
•
In multicellular plants and animals, the production of different transcription regulators in different cell types ensures the expression of
only those genes appropriate to the particular type of cell.
•
One differentiated cell type can be converted to another by artificially
expressing an appropriate set of transcription regulators. A differentiated cell can also be reprogrammed into a stem cell by artificially
expressing a particular set of such regulators.
•
Cells in multicellular organisms have mechanisms that enable their
progeny to “remember” what type of cell they should be. A prominent mechanism for propagating cell memory relies on transcription
regulators that perpetuate transcription of their own gene—a form of
positive feedback.
•
A master transcription regulator, if expressed in the appropriate precursor cell, can trigger the formation of a specialized cell type or
even an entire organ.
•
The pattern of DNA methylation can be transmitted from one cell
generation to the next, producing a form of epigenetic inheritance
that helps a cell remember the state of gene expression in its parent
cell. There is also evidence for a form of epigenetic inheritance based
on transmitted chromatin structures.
•
Cells can regulate gene expression by controlling events that occur
after transcription has begun. Many of these post-transcriptional
mechanisms rely on RNA molecules that can influence their own stability or translation.
•
MicroRNAs (miRNAs) control gene expression by base-pairing with
specific mRNAs and inhibiting their stability and translation.
•
Cells have a defense mechanism for destroying “foreign” doublestranded RNAs, many of which are produced by viruses. It makes use
of small interfering RNAs (siRNAs) that are produced from the foreign
RNAs in a process called RNA interference (RNAi).
•
Scientists can take advantage of RNAi to inactivate specific genes of
interest.
•
The recent discovery of thousands of long noncoding RNAs in
mammals has opened a new window to the roles of RNAs in gene
regulation.
Key terms
combinatorial control
promoter
differentiation
regulatory DNA sequence
DNA methylation
regulatory RNA
epigenetic inheritance
reporter gene
gene expressionRNA interference (RNAi)
long noncoding RNA
small interfering RNA (siRNA)
microRNA (miRNA)
transcription regulator
positive feedback loop
transcriptional activator
post-transcriptional control
transcriptional repressor
285
286
Chapter 8
Control of Gene Expression
Questions
Question 8–6
A virus that grows in bacteria (bacterial viruses are called
bacteriophages) can replicate in one of two ways. In the
prophage state, the viral DNA is inserted into the bacterial
chromosome and is copied along with the bacterial genome
each time the cell divides. In the lytic state, the viral DNA
is released from the bacterial chromosome and replicates
many times in the cell. This viral DNA then produces
viral coat proteins that together with the replicated viral
DNA form many new virus particles that burst out of the
bacterial cell. These two forms of growth are controlled by
two transcription regulators, called c1 (“c one”) and Cro,
that are encoded by the virus. In the prophage state, cI is
expressed; in the lytic state, Cro is expressed. In addition to
regulating the expression of other genes, c1 represses the
Cro gene, and Cro represses the c1 gene (Figure Q8–4).
When bacteria containing a phage in the prophage state are
briefly irradiated with UV light, c1 protein is degraded.
Your task in the laboratory of Professor Quasimodo is
to determine how far an enhancer (a binding site for an
activator protein) could be moved from the promoter
of the straightspine gene and still activate transcription.
You systematically vary the number of nucleotide pairs
between these two sites and then determine the amount of
transcription by measuring the production of Straightspine
mRNA. At first glance, your data look confusing (Figure
Q8–6). What would you have expected for the results of
this experiment? Can you save your reputation and explain
these results to Professor Quasimodo?
A.What will happen next?
B.Will the change in (A) be reversed when the UV light is
switched off?
amount of mRNA produced
Question 8–4
50
C.Why might this response to UV light have evolved?
c1 protein
60
70
80
90
100
110
number of nucleotides between enhancer and promoter
Figure Q8–6
Question 8–7
c1 gene
PROPHAGE
STATE
Cro gene
NO Cro GENE
TRANSCRIPTION
Cro protein
c1 gene
Cro gene
NO c1 GENE
TRANSCRIPTION
LYTIC
STATE
The λ repressor binds as a dimer to critical sites on the λ
ECB4 EQ8.07/Q8.07
genome to repress the virus’s lytic genes. This is necessary
to maintain the prophage (integrated) state. Each molecule
of the repressor consists of an N-terminal DNA-binding
domain and a C-terminal dimerization domain (Figure
Q8–7). Upon induction (for example, by irradiation with
UV light), the genes for lytic growth are expressed, λ
progeny are produced, and the bacterial cell is lysed (see
Question 8–4). Induction is initiated by cleavage of the
λ repressor at a site between the DNA-binding domain
and the dimerization domain, which causes the repressor
to dissociate from the DNA. In the absence of bound
repressor, RNA polymerase binds and initiates lytic growth.
Given that the number (concentration) of DNA-binding
domains is unchanged by cleavage of the repressor, why do
you suppose its cleavage results in its dissociation from the
DNA?
Figure Q8–4
Question 8–5
Which of the following statements are correct? Explain your
answers.
A.In bacteria, but not in eukaryotes, many mRNAs contain
ECB3
the coding region for
moreEQ8.04/Q8.04
than one gene.
C
N
+
C
C
N
repressor monomers
N
C
C
N
repressor dimer
N
cleavage
site
C
N
DNA binding site
Figure Q8–7
B.Most DNA-binding proteins bind to the major groove of
the DNA double helix.
Question 8–8
C.Of the major control points in gene expression
(transcription, RNA processing, RNA transport, translation,
and control of a protein’s activity), transcription initiation is
one of the most common.
The genes that encode the enzymes for arginine
biosynthesis are located at several positions around the
genome of E. coli,
andeQ8.09/Q8.09
they are regulated coordinately
ECB4
by a transcription regulator encoded by the ArgR gene.
Chapter 8 End-of-Chapter Questions
The activity of the ArgR protein is modulated by arginine.
Upon binding arginine, ArgR alters its conformation,
dramatically changing its affinity for the DNA sequences in
the promoters of the genes for the arginine biosynthetic
enzymes. Given that ArgR is a repressor protein, would you
expect that ArgR would bind more tightly or less tightly
to the DNA sequences when arginine is abundant? If ArgR
functioned instead as an activator protein, would you expect
the binding of arginine to increase or to decrease its affinity
for its regulatory DNA sequences? Explain your answers.
Question 8–9
Question 8–12
Imagine the two situations shown in Figure Q8–12. In
cell I, a transient signal induces the synthesis of protein
A, which is a transcriptional activator that turns on many
genes including its own. In cell II, a transient signal induces
the synthesis of protein R, which is a transcriptional
repressor that turns off many genes including its own. In
which, if either, of these situations will the descendants of
the original cell “remember” that the progenitor cell had
experienced the transient signal? Explain your reasoning.
(A) CELL I
When enhancers were initially found to influence
transcription many thousands of nucleotide pairs from
the promoters they control, two principal models were
invoked to explain this action at a distance. In the “DNA
looping” model, direct interactions between proteins bound
at enhancers and promoters were proposed to stimulate
transcription initiation. In the “scanning” or “entry-site”
model, RNA polymerase (or another component of the
transcription machinery) was proposed to bind at the
enhancer and then scan along the DNA until it reached the
promoter. These two models were tested using an enhancer
on one piece of DNA and a β-globin gene and promoter on
a separate piece of DNA (Figure Q8–9). The β-globin gene
was not expressed from the mixture of pieces. However,
when the two segments of DNA were joined via a linker
(made of a protein that binds to a small molecule called
biotin), the β-globin gene was expressed.
Does this experiment distinguish between the DNA
looping model and the scanning model? Explain your
answer.
biotin attached to one end of
each DNA molecule
β-globin gene
enhancer
+ avidin
transcription
enhancer
287
promoter
β-globin gene
Figure Q8–9
Question 8–10
Differentiated cells of an organism contain the same genes.
(Among the few exceptions to this rule are the cells of
ECB4 eQ8.11/Q8.11
the mammalian immune system, in which the formation of
specialized cells is based on limited rearrangements of the
genome.) Describe an experiment that substantiates the
first sentence of this question, and explain why it does.
Question 8–11
Figure 8–17 shows a simple scheme by which three
transcription regulators are used during development
to create eight different cell types. How many cell types
could you create, using the same rules, with four different
transcription regulators? As described in the text, MyoD is
a transcription regulator that by itself is sufficient to induce
muscle-specific gene expression in fibroblasts. How does
this observation fit the scheme in Figure 8–17?
OFF
A
gene activator
A
transient
signal
A
transient
signal
R
A
turns on transcription
of activator mRNA
A
activator protein
turns on its own
transcription
(B) CELL II
OFF
R
gene repressor
R
turns on transcription
of repressor mRNA
R
R
repressor protein
turns off its own
transcription
Figure Q8–12
Question 8–13
Discuss the following argument: “If the expression of every
gene depends on aECB4
set ofeQ8.14/Q8.14
transcription regulators, then the
expression of these regulators must also depend on the
expression of other regulators, and their expression must
depend on the expression of still other regulators, and so
on. Cells would therefore need an infinite number of genes,
most of which would code for transcription regulators.”
How does the cell get by without having to achieve the
impossible?
Page left intentionally blank
chapter nine
9
How Genes and Genomes
Evolve
For a given individual, the nucleotide sequence of the genome in virtually
every one of its cells is the same. But compare the DNA of two individuals—even parent and child—and that is no longer the case: the genomes
of individuals within a species contain slightly different information. And
between members of different species, the deviations are even more
extensive.
Such differences in DNA sequence are responsible for the diversity of life
on Earth, from the subtle variations in hair color, eye color, and skin color
that characterize members our own species (Figure 9–1) to the dramatic
differences in phenotype that distinguish a fish from a fungus or a robin
from a rose. But if all life emerged from a common ancestor—a singlecelled organism that existed some 3.5 billion years ago—where did these
genetic improvisations come from? How did they arise, why were they
preserved, and how do they contribute to the breathtaking biological
diversity that surrounds us?
Improvements in the methods used to sequence and analyze whole
genomes—from pufferfish and the plague bacterium to people from
around the world—are now allowing us to address some of these questions. In Chapter 10, we describe these revolutionary technologies, which
continue to transform the modern era of genomics. In this chapter, we
present some of the fruits of these technological innovations. Our ability
to compare the genomes of a wide-ranging collection of organisms has
provided striking confirmation of Darwin’s explanations for the diversity
of life on Earth—revealing how processes of mutation and natural selection have been sculpting DNA sequences for billions of years, giving rise
to the spectacular menagerie of present-day life-forms that crowd every
corner of the planet.
GENERATING GENETIC
VARIATION
reconstructing life’s
family tree
TRANSPOSONS AND VIRUSES
examining the human
genome
290
Chapter 9
How Genes and Genomes Evolve
In this chapter, we discuss how genes and genomes change over time.
We examine the molecular mechanisms that generate genetic diversity, and we consider how the information in present-day genomes can
be deciphered to yield a historical record of the evolutionary processes
that have shaped these DNA sequences. We take a brief look at mobile
genetic elements and consider how these elements, along with modernday viruses, can carry genetic information from place to place and from
organism to organism. Finally, we end the chapter by taking a closer look
at the human genome to see what our own DNA sequences tell us about
who we are and where we come from.
Figure 9–1 Small differences in DNA
sequence account for differences in
appearance between one individual and
the next. A group of English schoolchildren
displays a sampling of the characteristics
that define the unity and diversity of our
ECB4 e9.01/9.01
own species. (Courtesy of Fiona Pragoff,
Wellcome Images.)
Generating Genetic Variation
Evolution is more a tinkerer than an inventor: it uses as its raw materials the DNA sequences that each organism inherits from its ancestors.
There is no natural mechanism for making long stretches of entirely
novel nucleotide sequences. In this sense, no gene or genome is ever
entirely new. Instead, the astonishing diversity in form and function in
the living world is all the result of variations on preexisting themes. As
genetic variations pile up over millions of generations, they can produce
radical change.
Several basic types of genetic change are especially crucial in evolution
(Figure 9–2):
•
Mutation within a gene: An existing gene can be modified by a
mutation that changes a single nucleotide or deletes or duplicates
one or more nucleotides. These mutations can alter the splicing
of a gene’s transcript or change the stability, activity, location, or
interactions of its encoded protein or RNA product.
•
Mutation within regulatory DNA: When and where a gene is
expressed can be affected by a mutation in the stretches of DNA
sequence that regulate the gene’s activity (described in Chapter 8).
For example, humans and fish have a surprisingly large number of
genes in common, but changes in the regulation of those shared
genes underlie many of the most dramatic differences between
those species.
•
Gene duplication: An existing gene, a larger segment of DNA, or
even a whole genome can be duplicated, creating a set of closely
related genes within a single cell. As this cell and its progeny
divide, the original DNA sequence and its duplicate can acquire
additional mutations and thereby assume new functions and patterns of expression.
•
Exon shuffling: Two or more existing genes can be broken and
rejoined to make a hybrid gene containing DNA segments that
originally belonged to separate genes. In eukaryotes, the breaking
and rejoining often occurs within the long intron sequences, which
do not encode protein. Because intron sequences are removed by
RNA splicing, the breaking and joining do not have to be precise to
result in a functional gene.
•
Mobile genetic elements: Specialized DNA sequences that can move
from one chromosomal location to another can alter the activity or
regulation of a gene; they can also promote gene duplication, exon
shuffling, and other genome rearrangements.
•
Horizontal gene transfer: A piece of DNA can be transferred from
the genome of one cell to that of another—even to that of another
species. This process, which is rare among eukaryotes but common among bacteria, differs from the usual “vertical” transfer of
genetic information from parent to progeny.
Generating Genetic Variation
ORIGINAL GENOME
ALTERED GENOME
MUTATION
WITHIN A GENE
mutation
gene
regulatory
DNA
MUTATION IN
REGULATORY DNA
gene
mutation
Figure 9–2 Genes and genomes can be
altered by several different mechanisms.
Small mutations, duplications, deletions,
rearrangements, and even the infusion
of fresh genetic material all contribute to
genome evolution. Although the mobile
genetic element here is shown interrupting
a gene regulatory sequence, the movement
of these parasitic elements can promote
a variety of genetic variations, including
gene duplication, exon shuffling, and other
regulatory and structural alterations.
mRNA
GENE
DUPLICATION
gene
gene A
introns
+
exon
gene B
mobile genetic element
EXON
SHUFFLING
+
TRANSPOSITION
+
regulatory
DNA
+
gene
mutation
organism A
HORIZONTAL
TRANSFER
organism B
organism B with new
gene from organism A
Each of these forms of genetic variation—from the simple mutations that
occur within a gene to the more extensive duplications, deletions, rearrangements, and additions that occur within a genome—has played an
important part in the evolution of modern organisms. And they still play
that part today, as organisms continue to evolve. In this section, we discuss these basic mechanisms of genetic change, and we consider their
consequences for genome evolution. But first, we pause to consider the
e9.02/9.02that many organisms use to pass
contribution of sex—theECB4
mechanism
genetic information on to future generations.
In Sexually Reproducing Organisms, Only Changes to the
Germ Line Are Passed On To Progeny
For bacteria and unicellular organisms that reproduce mainly asexually,
the inheritance of genetic information is fairly straightforward. Each individual duplicates its genome and donates one copy to each daughter cell
when the individual divides in two. The family tree of such unicellular
organisms is simply a branching diagram of cell divisions that directly
links each individual to its progeny and to its ancestors.
291
Question 9–1
In this chapter, it is argued that
genetic variability is beneficial for
a species because it enhances that
species’ ability to adapt to changing
conditions. Why, then, do you think
that cells go to such great lengths
to ensure the fidelity of DNA
replication?
292
Chapter 9
How Genes and Genomes Evolve
Figure 9–3 Germ-line cells and somatic
cells have fundamentally different
functions. In sexually reproducing
organisms, genetic information is
propagated into the next generation
exclusively by germ-line cells (red). This
cell lineage includes the specialized
reproductive cells—the germ cells (eggs
and sperm, red half circles)—which contain
only half the number of chromosomes than
do the other cells in the body (full circles).
When two germ cells come together during
fertilization, they form a fertilized egg or
zygote (purple), which once again contains
a full set of chromosomes (discussed in
Chapter 19). The zygote gives rise to both
germ-line cells and to somatic cells (blue).
Somatic cells form the body of the organism
but do not contribute their DNA to the next
generation.
germ cell
germ cell
germ-line cells
germ-line cells
germ
cell
zygote
zygote
somatic cells
somatic cells
PARENT
OFFSPRING
For a multicellular organism that reproduces sexually, however, the family connections are considerably more complex. Although individual cells
within that organism divide, only the specialized reproductive cells—
the germ cells—carry a copy of its genome to the next generation of
organisms (discussed in Chapter 19). All the other cells of the body—the
ECB4 e9.03/9.03
somatic cells—are doomed to die without leaving evolutionary descendants of their own (Figure 9–3). In a sense, somatic cells exist only to help
the germ cells survive and propagate.
A mutation that occurs in a somatic cell—although it might have unfortunate consequences for the individual in which it occurs (causing cancer,
for example)—will not be transmitted to the organism’s offspring. For a
mutation to be passed on to the next generation, it must alter the germ
line—the cell lineage that gives rise to the germ cells (Figure 9–4). Thus,
when we track the genetic changes that accumulate during the evolution
of sexually reproducing organisms, we are looking at events that took
place in a germ-line cell. It is through a series of germ-line cell divisions
that sexually reproducing organisms trace their descent back to their
ancestors and, ultimately, back to the ancestors of us all—the first cells
that existed, at the origin of life more than 3.5 billion years ago.
In addition to perpetuating a species, sex also introduces its own form
of genetic change: when germ cells from a male and female unite during fertilization, they generate offspring that are genetically distinct from
either parent. We discuss this form of genetic diversification in detail
in Chapter 19. In the meantime, aside from this mating-based genome
germ cell
germ cell
germ-line cells
germ-line cells
A
Figure 9–4 Mutations in germ-line
cells and somatic cells have different
consequences. A mutation that occurs
in a germ-line cell (A) can be passed on
to the cell’s progeny and, ultimately, to
the progeny of the organism (green). By
contrast, a mutation that arises in a somatic
cell (B) affects only the progeny of that
cell (orange) and will not be passed on
to the organism’s progeny. As we discuss
in Chapter 20, somatic mutations are
responsible for most human cancers (see
pp. 714–717).
germ
cell
zygote
zygote
mutations
B
somatic cells
PARENT
somatic cells
OFFSPRING
Generating Genetic Variation
293
reshuffling, which influences how mutations are inherited in organisms
that reproduce sexually, most of the mechanisms that generate genetic
change are the same for all living things, as we now discuss.
Point Mutations Are Caused by Failures of the Normal
Mechanisms for Copying and Repairing DNA
Despite the elaborate mechanisms that exist to faithfully copy and repair
DNA sequences, each nucleotide pair in an organism’s genome runs a
small risk of changing each time a cell divides. Changes that affect a single nucleotide pair are called point mutations. These typically arise from
rare errors in DNA replication or repair (discussed in Chapter 6).
The point mutation rate has been determined directly in experiments with
bacteria such as E. coli. Under laboratory conditions, E. coli divides about
once every 20–25 minutes; in less than a day, a single E. coli can produce
more descendants than there are humans on Earth—enough to provide
a good chance for almost any conceivable point mutation to occur. A
culture containing 109 E. coli cells thus harbors millions of mutant cells
whose genomes differ subtly from the ancestor cell. Some of these mutations may confer a selective advantage on individual cells: resistance to
a poison, for example, or the ability to survive when deprived of a standard nutrient. By exposing the culture to a selective condition—adding an
antibiotic or removing an essential nutrient, for example—one can find
these needles in the haystack; that is, the cells that have undergone a
specific mutation enabling them to survive in conditions where the original cells cannot (Figure 9–5). Such experiments have revealed that the
overall point mutation frequency in E. coli is about 3 changes per 1010
nucleotide pairs each cell generation. The mutation rate in humans, as
determined by comparing the DNA sequences of children and their parents (and estimating how many times the parental germ cells divided), is
mutant E. coli cell
that cannot grow
in the absence of
INNOCULATE
histidine
CULTURE
MUTATION IN His GENE
TGA
ACT
UGA
stop codon
mutation eliminates
enzyme required to
make histidine
inactive
His
gene
mRNA
AS CELLS DIVIDE,
RANDOM MUTATIONS
ARISE SPONTANEOUSLY
rich medium,
which includes
histidine, allows
all bacteria
to multiply
SAMPLE OF CELLS
SPREAD ON
PETRI DISH
medium lacking
histidine
rare colony of revertant
cells that can grow in
absence of histidine
bacteria in which
different mutations
have occurred
REVERSION MUTATION
IN His GENE
ACC
active
His
gene
UGG
mRNA
TG G
enzyme
reversion mutation
restores production of
enzyme required to
make histidine
Figure 9–5 Mutation rates can be measured in the laboratory. In this experiment, an E. coli strain that carries a deleterious point
mutation in the His gene—which is needed to manufacture the amino acid histidine—is used. The mutation converts a G-C nucleotide
pair to an A-T, resulting in a premature stop signal in the mRNA produced from the mutant gene (left box). As long as histidine is
supplied in the growth medium, this strain can grow and divide normally. If a large number of mutant cells (say 1010) is spread on an
agar plate that lacks histidine, the great majority will die. The rare survivors will contain a “reversion” mutation (in which the A-T is
changed back to a G-C). This reversion corrects the original defect and now allows the bacterium to make the enzyme it needs to
survive in the absence of histidine. Such mutations happen by chance and only rarely, but the ability to work with very large numbers of
e9.05/9.05
E. coli cells makes it possible to detect this change andECB4
to accurately
measure its frequency.
294
Chapter 9
How Genes and Genomes Evolve
about one-third that of E. coli—which suggests that the mechanisms that
evolved to maintain genome integrity operate with an efficiency that does
not differ significantly in even distantly related species.
Point mutations can destroy a gene’s activity or—very rarely—improve it
(as shown in Figure 9–5). More often, however, they do neither of these
things. At many sites in the genome, a point mutation has absolutely
no effect on the organism’s appearance, viability, or ability to reproduce.
Such neutral mutations often fall in regions of the gene where the DNA
sequence is unimportant, including most of an intron’s sequence. In cases
where they occur within an exon, neutral mutations can change the third
position of a codon such that the amino acid it specifies is unchanged—or
is so similar that the protein’s function is unaffected.
Point Mutations Can Change the Regulation of a Gene
Mutations in the coding sequences of genes are fairly easy to spot
because they change the amino acid sequence of the encoded protein in
predictable ways. But mutations in regulatory DNA are more difficult to
recognize, because they don’t affect protein sequence and can be located
some distance from the coding sequence of the gene.
Despite these difficulties, many examples have been discovered where
point mutations in regulatory DNA have a profound effect on the protein’s production and thereby on the organism. For example, a small
number of people are resistant to malaria because of a point mutation
that affects the expression of a cell-surface receptor to which the malaria
parasite Plasmodium vivax binds. The mutation prevents the receptor
from being produced in red blood cells, rendering the individuals who
carry this mutation immune to malarial infection.
Point mutations in regulatory DNA also have a role in our ability to
digest lactose, the main sugar in milk. Our earliest ancestors were lactose intolerant, because the enzyme that breaks down lactose—called
lactase—was made only during infancy. Adults, who were no longer
exposed to breast milk, did not need the enzyme. When humans began to
get milk from domestic animals some 10,000 years ago, variant genes—
produced by random mutation—enabled those who carried the variation
to continue to express lactase as adults. We now know that people who
retain the ability to digest milk as adults contain a point mutation in the
regulatory DNA of the lactase gene, allowing it to be efficiently transcribed
throughout life. In a sense, these milk-drinking adults are “mutants” with
respect to their ability to digest lactose. It is remarkable how quickly this
trait spread through the human population, especially in societies that
depended heavily on milk for nutrition (Figure 9–6).
These evolutionary changes in the regulatory sequence of the lactase
gene occurred relatively recently (10,000 years ago), well after humans
became a distinct species. However, much more ancient changes in
regulatory sequences have occurred in other genes, and some of these
are thought to underlie many of the profound differences among species
(Figure 9–7).
DNA Duplications Give Rise to Families of Related Genes
Point mutations can influence the activity of an existing gene, but how
do new genes with new functions come into being? Gene duplication is
perhaps the most important mechanism for generating new genes from
old ones. Once a gene has been duplicated, each of the two copies is
free to accumulate mutations that might allow it to perform a slightly
different function—as long as the original activity of the gene is not lost.
This specialization of duplicated genes occurs gradually, as mutations
Generating Genetic Variation
295
percentage of population
that is
lactose tolerant
100%
90–99%
80–89%
70–79%
60–69%
50–59%
40–49%
30–39%
20–29%
10–19%
0–9%
no data
Native Americans
Indigenous Australians
Figure 9–6 The ability of adult humans to digest milk followed the domestication of cattle. Approximately
10,000 years ago, humans in northern Europe and central Africa began to raise cattle. The subsequent availability
of cow’s milk—particularly during periods of starvation—gave a selective advantage to those humans able to digest
lactose as adults. Two independent point mutations that allow the expression of lactase in adults arose in human
populations—one in northern Europe and another in central Africa. These mutations have since spread through
different regions of the world. For example, the migration of Northern Europeans to North America and Australia
explains why most people living on these continents can digest lactose as adults; the native populations of North
America and Australia, however, remain lactose intolerant.
ECB4 e9.06/9.06
accumulate in the descendants of the original
cell in which gene duplication occurred. By repeated rounds of this process of gene duplication
and divergence over many millions of years, one gene can give rise to a
whole family of genes, each with a specialized function, within a single
genome. Analysis of genome sequences reveals many examples of such
gene families: in Bacillus subtilis, for example, nearly half of the genes
have one or more obvious relatives elsewhere in the genome. And in
vertebrates, the globin family of genes, which encode oxygen-carrying
proteins, clearly arose from a single primordial gene, as we see shortly.
But how does gene duplication occur in the first place?
ORGANISM A
RELATED ORGANISM B
embryonic stage 1
gene 1
embryonic stage 1
gene 2
gene 3
gene 1
gene 2
gene 3
regulatory DNA sequences
transcription
regulator turns
on gene 1
PRODUCT OF GENE 1
TURNS ON GENE 3
transcription
regulator
embryonic stage 2
gene 1
(A)
(B)
gene 2
gene 3
PRODUCT OF GENE 1
TURNS ON GENE 2
embryonic stage 2
gene 1
gene 2
gene 3
Figure 9–7 Changes in regulatory
DNA sequences can have dramatic
consequences for the development
of an organism. (A) In this hypothetical
example, the genomes of organisms
A and B contain the same three genes
(1, 2, and 3) and encode the same two
transcription regulators (red oval, brown
triangle). However, the regulatory DNA
controlling expression of genes 2 and
3 is different in the two organisms.
Although both express the same gene—
gene 1—during embryonic stage 1,
the differences in their regulatory DNA
cause them to express different genes
in stage 2. (B) In principle, a collection
of such regulatory changes can have
profound effects on an organism’s
developmental program—and,
ultimately, on the appearance of the
adult.
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Chapter 9
How Genes and Genomes Evolve
Figure 9–8 Gene duplication can be
caused by crossovers between short,
repeated DNA sequences in adjacent
homologous chromosomes. The two
chromosomes shown here undergo
homologous recombination at short
repeated sequences (red ), that bracket a
gene (orange). These repeated sequences
can be remnants of mobile genetic
elements, which are present in many copies
in the human genome, as we discuss shortly.
When crossing-over occurs unequally, as
shown, one chromosome will get two copies
of the gene, while the other will get none.
The type of homologous recombination
that produces gene duplications is called
unequal crossing-over because the resulting
products are unequal in size. If this process
occurs in the germ line, some progeny will
inherit the long chromosome, while others
will inherit the short